SitesBLAST

Q7XSN8 Serine racemase; D-serine dehydratase; D-serine ammonia-lyase; L-serine dehydratase; L-serine ammonia-lyase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Oryza sativa subsp. japonica (Rice) (see paper)
39% identity, 90% coverage: 17:323/342 of query aligns to 24:334/339 of Q7XSN8

query
sites
Q7XSN8

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E219 (≠ Q212) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ A218) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
42% identity, 92% coverage: 17:329/342 of query aligns to 12:326/326 of 2gn2A

query
sites
2gn2A

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active site: K56 (= K61), A81 (= A86), Q207 (= Q212), V211 (≠ A216), G213 (≠ A218), G235 (= G240), I308 (≠ V311), S309 (= S312)
binding cytidine-5'-monophosphate: R51 (≠ K56), T52 (= T57), G53 (= G58), A114 (= A119), D117 (≠ G122), Y118 (= Y123), N312 (= N315)

O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
40% identity, 91% coverage: 17:326/342 of query aligns to 13:322/323 of O59791

query
sites
O59791

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K57 (= K61) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ A86) active site, Proton acceptor; mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity.
N84 (= N88) binding pyridoxal 5'-phosphate
G183 (= G187) binding pyridoxal 5'-phosphate
G184 (= G188) binding pyridoxal 5'-phosphate
G185 (= G189) binding pyridoxal 5'-phosphate
G186 (= G190) binding pyridoxal 5'-phosphate
L187 (= L191) binding pyridoxal 5'-phosphate
E208 (≠ Q212) binding Mg(2+)
G212 (≠ A216) binding Mg(2+)
D214 (≠ A218) binding Mg(2+)
S308 (= S312) binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
40% identity, 91% coverage: 17:326/342 of query aligns to 8:317/318 of 1wtcA

query
sites
1wtcA

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Q

K

I

L

D

K

S

N

R

K

H

R

C

I

G

G

V

I

I

I

V
x
I

S
|
S

G

G

N

N

F

V

D

D

I

I

S

E

R

R

M

Y

A

A

E

H

I

F

Q

L

S

S

active site: K52 (= K61), S77 (≠ A86), E203 (≠ Q212), G207 (≠ A216), D209 (≠ A218), G231 (= G240), I302 (≠ V311), S303 (= S312)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ H29), K47 (= K56), M48 (≠ T57), A109 (≠ E118), A110 (= A119), Y114 (= Y123)
binding magnesium ion: E203 (≠ Q212), G207 (≠ A216), D209 (≠ A218)
binding pyridoxal-5'-phosphate: F51 (= F60), K52 (= K61), N79 (= N88), G178 (= G187), G179 (= G188), G180 (= G189), G181 (= G190), G231 (= G240), E276 (= E285), T278 (≠ A287), S303 (= S312)

1v71A Crystal structure of s.Pombe serine racemase
40% identity, 91% coverage: 17:326/342 of query aligns to 8:317/318 of 1v71A

query
sites
1v71A

V

V

H

A

D

S

A

A

W

S

K

E

R

R

L

I

D

K

P

K

V

F

V

A

H

N

Q

K

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

T

T

V

N

N

L

K

R

E

T

F

G

V

K

A

N

E

I

V

Y

F

F

F

K

K

M

C

E

E

N

N

Q

F

Q

Q

K

K

T

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

S

L

Y

N

K

A

L

L

M

S

R

Q

L

L

S

N

P

E

K

A

E

Q

L

R

D

K

R

A

G

G

V

V

I

L

T

T

A

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

L

I

A

A

L

L

A

S

A

A

Y

K

K

I

L

L

G

G

V

I

K

P

A

A

T

K

I

I

Y

I

M

M

A

P

E

L

A

D

T

A

P

P

E

E

A

A

K

K

V

V

E

A

A

A

T

T

R

K

G

G

Y

Y

G

G

A

G

E

Q

V

V

V

I

L

M

T

Y

G

-

E

D

S

R

F

Y

Q

K

E

D

A

D

F

R

E

E

A

K

S

M

L

A

K

K

Q

E

-

I

Q

S

E

E

R

R

C

E

G

G

A

L

T

T

Y

I

V

I

H

P

P

P

F

Y

D

D

D

H

Y

P

D

H

I

V

M

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

L

L

L

F

E

E

Q

E

V

V

N

G

T

P

I

L

D

D

T

A

I

L

V

F

V

V

P

C

I

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

V

L

G

A

A

A

K

R

S

H

V

F

N

A

P

P

D

N

I

C

K

E

V

V

I

Y

G

G

V

V

Q
x
E

A

P

K

E

A

A

A
x
G

P

N

A
x
D

M

G

H

Q

T

Q

A

S

Y

F

H

R

R

K

G

G

V

S

V

I

K

V

K

H

L

I

D

D

K

T

V

P

S

K

T

T

I

I

A

A

E

D

G
|
G

I

A

A

Q

V

T

K

Q

Q

H

P

L

G

G

E

N

N

Y

T

T

L

F

P

S

L

I

I

I

N

K

N

E

Y

K

V

V

D

D

I

I

I

L

T

T

V

V

S

S

E

D

E

E

I

L

A

I

D

D

A

C

I

L

V

K

N

F

M

Y

L

A

E

A

R

R

G

M

K

K

S

I

L

V

V

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

A

S

F

F

A

A

G

A

L

A

L

R

S

A

H

M

N

K

D

E

Q

K

I

L

D

K

S

N

R

K

H

R

C

I

G

G

V

I

I

I

V
x
I

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

I

S

E

R

R

M

Y

A

A

E

H

I

F

Q

L

S

S

active site: K52 (= K61), S77 (≠ A86), E203 (≠ Q212), G207 (≠ A216), D209 (≠ A218), G231 (= G240), I302 (≠ V311), S303 (= S312)
binding magnesium ion: E203 (≠ Q212), G207 (≠ A216), D209 (≠ A218)
binding pyridoxal-5'-phosphate: F51 (= F60), K52 (= K61), N79 (= N88), G178 (= G187), G179 (= G188), G180 (= G189), G181 (= G190), G231 (= G240), E276 (= E285), T278 (≠ A287), S303 (= S312), G304 (= G313)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
40% identity, 91% coverage: 17:326/342 of query aligns to 9:318/319 of 2zr8A

query
sites
2zr8A

V

V

H

A

D

S

A

A

W

S

K

E

R

R

L

I

D

K

P

K

V

F

V

A

H

N

Q

K

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

T

T

V

N

N

L

K

R

E

T

F

G

V

K

A

N

E

I

V

Y

F

F

F

K

K

M

C

E

E

N

N

Q

F

Q

Q

K

K

T

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

S

L

Y

N

K

A

L

L

M

S

R

Q

L

L

S

N

P

E

K

A

E

Q

L

R

D

K

R

A

G

G

V

V

I

L

T

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

L

I

A

A

L

L

A

S

A

A

Y

K

K

I

L

L

G

G

V

I

K

P

A

A

T

K

I

I

Y

I

M

M

A

P

E

L

A

D

T

A

P

P

E

E

A

A

K

K

V

V

E

A

A

A

T

T

R

K

G

G

Y

Y

G

G

A

G

E

Q

V

V

V

I

L

M

T

Y

G

-

E

D

S

R

F

Y

Q

K

E

D

A

D

F
x
R

E

E

A

K

S

M

L

A

K

K

Q

E

-

I

Q

S

E

E

R

R

C

E

G

G

A

L

T

T

Y

I

V

I

H

P

P
|
P

F

Y

D

D

D

H

Y

P

D

H

I

V

M

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

L

L

L

F

E

E

Q

E

V

V

N

G

T

P

I

L

D

D

T

A

I

L

V

F

V

V

P

C

I

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

V

L

G

A

A

A

K

R

S

H

V

F

N

A

P

P

D

N

I

C

K

E

V

V

I

Y

G

G

V

V

Q
x
E

A

P

K

E

A

A

A
x
G

P

N

A
x
D

M

G

H

Q

T

Q

A

S

Y

F

H

R

R

K

G

G

V

S

V

I

K

V

K

H

L

I

D

D

K

T

V

P

S

K

T

T

I

I

A

A

E
x
D

G
|
G

I
x
A

A
x
Q

V
x
T

K

Q

Q

H

P

L

G

G

E

N

N

Y

T

T

L

F

P

S

L

I

I

I

N

K

N

E

Y

K

V

V

D

D

I

I

I

L

T

T

V

V

S

S

E

D

E

E

I

L

A

I

D

D

A

C

I

L

V

K

N

F

M

Y

L

A

E

A

R

R

G

M

K

K

S

I

L

V

V

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

A

S

F

F

A

A

G

A

L

A

L

R

S

A

H

M

N

K

D

E

Q

K

I

L

D

K

S

N

R

K

H

R

C

I

G

G

V

I

I

I

V
x
I

S
|
S

G

G

N

N

F

V

D

D

I

I

S

E

R

R

M

Y

A

A

E

H

I

F

Q

L

S

S

active site: K53 (= K61), S78 (≠ A86), E204 (≠ Q212), G208 (≠ A216), D210 (≠ A218), G232 (= G240), I303 (≠ V311), S304 (= S312)
binding magnesium ion: E204 (≠ Q212), G208 (≠ A216), D210 (≠ A218)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F60), K53 (= K61), S77 (= S85), S78 (≠ A86), N80 (= N88), H81 (= H89), P147 (= P155), G179 (= G187), G180 (= G188), G181 (= G189), G182 (= G190), G232 (= G240), E277 (= E285), T279 (≠ A287), S304 (= S312)
binding serine: S78 (≠ A86), R129 (≠ F138), D231 (≠ E239), G232 (= G240), A233 (≠ I241), Q234 (≠ A242), T235 (≠ V243)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
40% identity, 91% coverage: 17:326/342 of query aligns to 9:318/319 of 2zpuA

query
sites
2zpuA

V

V

H

A

D

S

A

A

W

S

K

E

R

R

L

I

D

K

P

K

V

F

V

A

H

N

Q

K

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

T

T

V

N

N

L

K

R

E

T

F

G

V

K

A

N

E

I

V

Y

F

F

F

K

K

M

C

E

E

N

N

Q

F

Q

Q

K

K

T

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

S

L

Y

N

K

A

L

L

M

S

R

Q

L

L

S

N

P

E

K

A

E

Q

L

R

D

K

R

A

G

G

V

V

I

L

T

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

L

I

A

A

L

L

A

S

A

A

Y

K

K

I

L

L

G

G

V

I

K

P

A

A

T

K

I

I

Y

I

M

M

A

P

E

L

A

D

T

A

P

P

E

E

A

A

K

K

V

V

E

A

A

A

T

T

R

K

G

G

Y

Y

G

G

A

G

E

Q

V

V

V

I

L

M

T

Y

G

-

E

D

S

R

F

Y

Q

K

E

D

A

D

F

R

E

E

A

K

S

M

L

A

K

K

Q

E

-

I

Q

S

E

E

R

R

C

E

G

G

A

L

T

T

Y

I

V

I

H

P

P
|
P

F

Y

D

D

D

H

Y

P

D

H

I

V

M

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

L

L

L

F

E

E

Q

E

V

V

N

G

T

P

I

L

D

D

T

A

I

L

V

F

V

V

P

C

I

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

V

L

G

A

A

A

K

R

S

H

V

F

N

A

P

P

D

N

I

C

K

E

V

V

I

Y

G

G

V

V

Q
x
E

A

P

K

E

A

A

A
x
G

P

N

A
x
D

M

G

H

Q

T

Q

A

S

Y

F

H

R

R

K

G

G

V

S

V

I

K

V

K

H

L

I

D

D

K

T

V

P

S

K

T

T

I

I

A

A

E

D

G
|
G

I

A

A

Q

V

T

K

Q

Q

H

P

L

G

G

E

N

N

Y

T

T

L

F

P

S

L

I

I

I

N

K

N

E

Y

K

V

V

D

D

I

I

I

L

T

T

V

V

S

S

E

D

E

E

I

L

A

I

D

D

A

C

I

L

V

K

N

F

M

Y

L

A

E

A

R

R

G

M

K

K

S

I

L

V

V

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

A

S

F

F

A

A

G

A

L

A

L

R

S

A

H

M

N

K

D

E

Q

K

I

L

D

K

S

N

R

K

H

R

C

I

G

G

V

I

I

I

V
x
I

S
|
S

G

G

N

N

F

V

D

D

I

I

S

E

R

R

M

Y

A

A

E

H

I

F

Q

L

S

S

active site: K53 (= K61), S78 (≠ A86), E204 (≠ Q212), G208 (≠ A216), D210 (≠ A218), G232 (= G240), I303 (≠ V311), S304 (= S312)
binding magnesium ion: E204 (≠ Q212), G208 (≠ A216), D210 (≠ A218)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F60), K53 (= K61), S77 (= S85), S78 (≠ A86), N80 (= N88), H81 (= H89), P147 (= P155), G179 (= G187), G180 (= G188), G181 (= G189), G182 (= G190), G232 (= G240), E277 (= E285), T279 (≠ A287), S304 (= S312)

A4F2N8 L-threo-3-hydroxyaspartate ammonia-lyase; L-threo-3-hydroxyaspartate dehydratase; L-THA DH; EC 4.3.1.16 from Pseudomonas sp. (see paper)
38% identity, 90% coverage: 18:324/342 of query aligns to 7:316/319 of A4F2N8

query
sites
A4F2N8

H

H

D

D

A

V

W

I

K

K

-

A

-

E

R

R

L

L

D

E

P

G

V

F

V

A

H

N

Q

R

T

T

P

P

I

V

R

F

T

T

S

S

A

R

T

T

T

L

N

D

L

A

R

E

T

T

G

G

K

A

N

Q

I

V

Y

F

F

I

K

K

M

C

E

E

N

N

Q

L

Q

Q

K

R

T

T

G

G

A

S

F

F

K
|
K

F

F

R

R

G

G

A

A

S

F

Y

N

K

A

L

L

M

S

R

R

L

F

S

D

P

E

K

A

E

Q

L

R

D

K

R

A

G

G

V

V

I

V

T

A

A

F

S

S

A

S

G

G

N

N

H

H

A

A

Q

Q

G

G

L

I

A

A

L

L

A

A

Y

R

K

L

L

L

G

Q

V

M

K

P

A

A

T

T

I

I

Y

V

M

M

A

P

E

T

A

D

T

A

P

P

E

A

A

A

K

K

V

V

E

A

A

A

T

T

R

R

G

E

Y

Y

G

G

A

A

E

T

V

V

L

F

T

Y

G

D

E

R

S

I

F

T

Q

E

E

D

A

R

F

E

E

Q

A

I

S

G

L

R

K

T

Q

L

Q

A

E

E

R

Q

C

H

G

G

A

M

T

T

Y

L

V

I

H

P

P

S

F

Y

D

D

D

H

Y

P

D

D

I

V

M

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

L

L

E

E

Q

F

V

T

N

G

T

P

I

L

D

D

T

A

I

L

V

F

V

V

P

G

I

L

G

G

L

M

I

L

S

S

G

G

I

T

A

A

V

L

G

A

A

T

K

R

S

A

V

L

N

S

P

P

D

D

I

C

K

L

V

L

I

Y

G

G

V

V

Q

E

A

P

K

E

A

A

A

G

P

N

A

D

M

G

H

Q

T

R

A

S

Y

F

H

Q

R

T

G

G

V

S

V

I

K

V

K

H

L

I

D

D

K

T

V

P

S

A

T

T

I

I

A

A

E

D

G

G

I

A

A

Q

V

T

K

Q

Q

H

P

L

G

G

E

N

N

H

T

T

L

F

P

P

L

I

I

I

N

R

N

E

Y

N

V

V

D

N

D

D

I

I

I

L

T

T

V

V

S

S

E

D

E

A

E

E

I

L

A

V

D

E

A

S

I

M

V

R

N

F

M

F

L

M

E

Q

R

R

G

M

K

K

S

M

L

V

V

V

E

E

G

P

A

T

G

G

A

C

A

L

A

G

F

L

A

A

G

A

L

L

L

R

S

N

H

L

N

K

D

Q

Q

Q

I

F

D

R

S

G

R

Q

H

R

C

V

G

G

V

I

I

I

V

V

S

T

G

G

N

N

F

V

D

D

I

I

S

E

R

K

M

Y

A

A

E

S

I

L

K53 (= K61) mutation to A: Loss of enzymatic activity.

Q9GZT4 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Homo sapiens (Human) (see 4 papers)
38% identity, 85% coverage: 28:319/342 of query aligns to 23:320/340 of Q9GZT4

query
sites
Q9GZT4

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S
|
S

A
x
S

T
x
I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K
|
K

T
|
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P
|
P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T
|
T

A

H

S

S

A

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D
|
D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G

G

I

V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N
|
N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K
|
K

S

L

L

L

V

I

E

E

G

P

A

T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V

L

S
|
S

G

G

N
|
N

F

V

D

D

I

L

S

T

S31 (= S36) binding ATP
S32 (≠ A37) binding ATP
I33 (≠ T38) binding ATP
K51 (= K56) binding ATP
T52 (= T57) binding ATP
K56 (= K61) modified: N6-(pyridoxal phosphate)lysine
P69 (= P74) binding Ca(2+)
T81 (= T83) binding Ca(2+)
N86 (= N88) binding pyridoxal 5'-phosphate
Q89 (= Q91) binding ATP
Y121 (= Y123) binding ATP
D178 (= D180) binding Mg(2+)
G185 (= G187) binding pyridoxal 5'-phosphate
G186 (= G188) binding pyridoxal 5'-phosphate
G187 (= G189) binding pyridoxal 5'-phosphate
G188 (= G190) binding pyridoxal 5'-phosphate
M189 (≠ L191) binding pyridoxal 5'-phosphate
E210 (≠ Q212) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (= A216) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ A218) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (= N249) binding Ca(2+); binding Mg(2+)
K279 (= K281) binding ATP
S313 (= S312) binding pyridoxal 5'-phosphate
N316 (= N315) binding ATP

Sites not aligning to the query:

13 binding Mg(2+)

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/320 of 7nbhAAA

query
sites
7nbhAAA

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K

K

T

T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K
|
K

V

K

E

L

A

A

T
x
I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G

G

L

M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E
x
D

G
|
G

I

V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N

N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E

E

G
x
P

A

T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G

G

N
|
N

F
x
V

D
|
D

I

L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A86), G85 (≠ A90), Q86 (= Q91), K111 (= K116), I115 (≠ T120), Y118 (= Y123), D235 (≠ E239), P281 (≠ G286), N313 (= N315), V314 (≠ F316), D315 (= D317)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/322 of 7nbgAAA

query
sites
7nbgAAA

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I
|
I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K
|
K

V

K

E

L

A

A

T
x
I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N

N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E

E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N83 (= N88), G182 (= G187), G183 (= G188), G184 (= G189), G185 (= G190), M186 (≠ L191), G236 (= G240), V237 (≠ I241), T282 (≠ A287), S310 (= S312), G311 (= G313)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A86), G85 (≠ A90), Q86 (= Q91), I101 (= I106), K111 (= K116), I115 (≠ T120), Y118 (= Y123)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/323 of 7nbfAAA

query
sites
7nbfAAA

V

I

H
|
H

Q
x
L

T
|
T

P
|
P

I

V

R
x
L

T
|
T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q
x
F

Q

Q

K

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N
|
N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E

E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding magnesium ion: N244 (= N249)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N83 (= N88), G182 (= G187), G183 (= G188), G184 (= G189), G185 (= G190), M186 (≠ L191), G236 (= G240), V237 (≠ I241), T282 (≠ A287), S310 (= S312), G311 (= G313)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (= H29), L22 (≠ Q30), T23 (= T31), P24 (= P32), L26 (≠ R34), T27 (= T35), F46 (≠ Q54)

Sites not aligning to the query:

binding magnesium ion: 3

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/323 of 7nbdAAA

query
sites
7nbdAAA

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N
|
N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L
x
W

E

E

R

R

G

M

K

K

S

L

L
|
L

V

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F
x
V

D

D

I
x
L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ L277), L278 (= L283), V314 (≠ F316), L316 (≠ I318)
binding magnesium ion: N244 (= N249)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N83 (= N88), G182 (= G187), G183 (= G188), G184 (= G189), G185 (= G190), M186 (≠ L191), G236 (= G240), V237 (≠ I241), E280 (= E285), T282 (≠ A287), S310 (= S312), G311 (= G313)

Sites not aligning to the query:

binding magnesium ion: 3

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/323 of 7nbcCCC

query
sites
7nbcCCC

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T
|
T

A
x
H

S

S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V
|
V

H
|
H

P
|
P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N

N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E

E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding biphenyl-4-ylacetic acid: T78 (= T83), H79 (≠ A84), H84 (= H89), V148 (= V153), H149 (= H154), P150 (= P155)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N83 (= N88), G182 (= G187), G183 (= G188), G184 (= G189), G185 (= G190), M186 (≠ L191), G236 (= G240), V237 (≠ I241), T282 (≠ A287), S310 (= S312), G311 (= G313)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:317/323 of 7nbcAAA

query
sites
7nbcAAA

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S

S

A

S

T

I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

V

P

P

K

D

E

A

L

L

D

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A

R

F

E

E

N

A

V

S

A

L

K

K

R

Q

V

Q

T

E

E

R

E

C

T

G

E

A

G

T

I

Y

M

V

V

H

H

P

P

F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

L

I

V

D

D

T

A

I

L

V

V

P

P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N
|
N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E

E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

L

S

T

active site: K53 (= K61), S81 (≠ A86), E207 (≠ Q212), A211 (= A216), D213 (≠ A218), G236 (= G240), L309 (≠ V311), S310 (= S312)
binding calcium ion: E207 (≠ Q212), A211 (= A216), D213 (≠ A218)
binding magnesium ion: N244 (= N249)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N83 (= N88), G182 (= G187), G183 (= G188), G184 (= G189), G185 (= G190), M186 (≠ L191), G236 (= G240), V237 (≠ I241), T282 (≠ A287), S310 (= S312), G311 (= G313)

Sites not aligning to the query:

binding magnesium ion: 3

6zspAAA serine racemase bound to atp and malonate. (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 20:310/320 of 6zspAAA

query
sites
6zspAAA

V

I

H

H

Q

L

T

T

P

P

I

V

R

L

T

T

S
|
S

A
x
S

T
x
I

T

L

N

N

L

Q

R

L

T

T

G

G

K

R

N

N

I

L

Y

F

F

F

K

K

M

C

E

E

N

L

Q

F

Q

Q

K
|
K

T
|
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

K

P

P

K

K

E

-

L

-

D

-

R

-

G

A

V

V

I

V

T

T

A

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

V

I

K

P

A

A

T

Y

I

I

Y

V

M

V

A

P

E

Q

A

T

T

A

P

P

E

D

A

C

K

K

V

K

E

L

A

A

T

I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

L

Y

T

C

G

E

E

P

S

S

F

D

Q

E

E

S

A
x
R

F

E

E

N

A

V

S

A

L

K

K

R

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Q

T

E

E

R

E

C

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E

A

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T

I

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M

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V

H

H

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F

N

D

Q

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E

Y

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D

A

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M

I

A

A

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G

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Q

G

G

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T

I

I

A

A

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E

E

L

V

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L

E

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Q

Q

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N

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A

I

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P

I

V

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G

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M

I

L

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A

G

G

I

I

A

A

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I

G

T

A

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K

S

A

V

L

N

K

P

P

D

S

I

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K

K

V

V

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G

A

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A

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x
E

A

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A

N

A
|
A

P

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A
x
D

M

C

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Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I

V

A

K

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-

K
x
S

Q

S

P

I

G

G

E

L

N

N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

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T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

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L

W

E
|
E

R
|
R

G

M

K
|
K

S

L

L

L

V

I

E

E

G

P

A

T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

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I

I

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V
x
L

S
|
S

G

G

N
|
N

F

V

D

D

I

L

S

T

active site: K53 (= K61), S74 (≠ A86), E200 (≠ Q212), A204 (= A216), D206 (≠ A218), G229 (= G240), L302 (≠ V311), S303 (= S312)
binding adenosine-5'-triphosphate: S28 (= S36), S29 (≠ A37), I30 (≠ T38), K48 (= K56), T49 (= T57), Q79 (= Q91), Y111 (= Y123), E266 (= E278), R267 (= R279), K269 (= K281), N306 (= N315)
binding magnesium ion: E200 (≠ Q212), A204 (= A216), D206 (≠ A218)
binding malonate ion: K53 (= K61), S73 (= S85), S74 (≠ A86), N76 (= N88), H77 (= H89), R125 (≠ A137), G229 (= G240), S232 (≠ K244)

5cvcA Structure of maize serine racemase (see paper)
39% identity, 92% coverage: 17:332/342 of query aligns to 8:325/329 of 5cvcA

query
sites
5cvcA

V

I

H

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D

E

A

A

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K

A

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R

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I

D

A

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H

Q

R

T

T

P

P

I

V

R

M

T

S

S

S

A

T

T

S

T

I

N

D

L

A

R

M

T

V

G

G

K

K

N

K

I

L

Y

F

F

F

K

K

M

C

E

E

N

C

Q

F

Q

Q

K

K

T

A

G

G

A

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

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S

Y

N

K

S

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I

M

F

R

A

L

L

S

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P

D

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E

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L

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D

S

R

K

G

G

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

A

G

A

L

V

A

A

L

L

A

A

Y

K

K

L

L

R

G

G

V

I

K

P

A

A

T

H

I

I

Y

V

M

I

A

P

E

R

A

N

T

A

P

P

E

A

A

S

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K

V

V

E

E

A

N

T

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R

K

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C

Y

Y

G

G

A

G

E

H

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I

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S

G

D

E

A

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S

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I

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E

E

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A

R

F

E

E

Y

A

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S

S

L

K

K

R

Q

V

Q

Q

E

E

R

E

C

T

G

G

A

A

T

V

Y

L

V

I

H

H

P

P

F

I

D

N

D

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Y

K

D

Y

I

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M

I

A

S

G

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G

G

T

T

I

V

A

S

L

L

E

E

L

L

E

E

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Q

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V

N

P

T

E

I

I

D

D

T

T

I

I

V

I

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V

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P

I

I

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x
S

G
|
G

L

L

I

I

S

S

G

G

I

V

A

A

V

L

G

A

A

A

K

K

S

A

V

I

N

N

P

P

D

S

I

I

K

R

V

I

I

L

G

A

V

A

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x
E

A

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A

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A
|
A

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D

A
x
D

M

S

H

A

T

Q

A

S

Y

K

H

A

R

A

G

G

V

K

V

I

K

I

K

T

L

L

D

P

K

S

V

T

S

N

T

T

I

I

A

A

E

D

G
|
G

I
x
L

A

R

V

A

K

F

Q

L

P

-

G

G

E

D

N

L

T

T

L

W

P

P

L

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I

V

N

R

N

D

Y

L

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V

D

D

I

V

I

I

T

V

V

V

S

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E

D

E

T

E

A

I

I

A

V

D

D

A

A

I

M

V

K

N

M

M

C

L

Y

E

E

R

I

G

L

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K

S

V

L

A

V

V

E
|
E

G

P

A

S

G

G

A

A

A

I

A

G

F

L

A

A

G

A

L

A

L

L

S

S

H

-

N

-

D

D

Q

E

I

F

-

K

-

Q

-

S

-

A

-

W

-

H

D

E

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S

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S

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K

C

I

G

G

V

I

I

I

V
|
V

S
|
S

G
|
G

G

G

N

N

F

V

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D

I

L

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G

R

T

M

L

A

-

E

-

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K

Q

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L

K

E

active site: K52 (= K61), S77 (≠ A86), E203 (≠ Q212), A207 (= A216), D209 (≠ A218), G231 (= G240), V306 (= V311), S307 (= S312)
binding magnesium ion: E203 (≠ Q212), A207 (= A216), D209 (≠ A218)
binding pyridoxal-5'-phosphate: F51 (= F60), K52 (= K61), N79 (= N88), S178 (≠ G187), G179 (= G188), G180 (= G189), G181 (= G190), L232 (≠ I241), E275 (= E285), S307 (= S312), G308 (= G313)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
38% identity, 85% coverage: 28:319/342 of query aligns to 21:313/322 of 3l6bA

query
sites
3l6bA

V

I

H

H

Q

L

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T

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P

I

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T

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S

A

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I

T

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N

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T

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R

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N

I

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Y

F

F

F

K

K

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E

E

N

L

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F

Q

Q

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K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

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M

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L

S

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K

E

P

L

-

D

-

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G

A

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S

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x
S

G

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|
N

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|
H

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Q

G

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L

L

A

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L

Y

A

A

Y

K

K

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E

G

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A

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Y

I

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K

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Y

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G

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x
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A

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K

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Q

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E

E

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E

C

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E

A

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E

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A

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Q

G

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T

I

I

A

A

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E

L

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L

E

N

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|
G

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x
M

I

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G

G

I

I

A

A

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K

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K

P

P

D

S

I

V

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K

V

V

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Y

G

A

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x
E

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A
|
A

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x
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T

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A

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Y

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K

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G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N

N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

I

L

S

T

active site: K54 (= K61), S77 (≠ A86), E203 (≠ Q212), A207 (= A216), D209 (≠ A218), G232 (= G240), T278 (≠ A287), L305 (≠ V311), S306 (= S312)
binding malonate ion: K54 (= K61), S76 (= S85), S77 (≠ A86), N79 (= N88), H80 (= H89), R128 (≠ A137), G232 (= G240)
binding manganese (ii) ion: E203 (≠ Q212), A207 (= A216), D209 (≠ A218)
binding pyridoxal-5'-phosphate: F53 (= F60), K54 (= K61), N79 (= N88), G178 (= G187), G179 (= G188), G180 (= G189), G181 (= G190), M182 (≠ L191), V233 (≠ I241), E276 (= E285), T278 (≠ A287), S306 (= S312), G307 (= G313)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
38% identity, 85% coverage: 28:317/342 of query aligns to 20:310/310 of 7nbgDDD

query
sites
7nbgDDD

V

I

H

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N

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R

N

N

I

L

Y

F

F

F

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K

M

C

E

E

N

L

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F

Q

Q

K

K

T

T

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G

A

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F
|
F

K
|
K

F

I

R

R

G

G

A

A

S

L

Y

N

K

A

L

V

M

R

R

S

L

L

S

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P

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K

E

P

L

-

D

-

R

K

G

A

V

V

I

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

L

L

A

T

L

Y

A

A

Y

K

K

L

L

E

G

G

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I

K

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A

A

T

Y

I
|
I

Y

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M

V

A

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E

Q

A

T

T

A

P

P

E

D

A

C

K

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K

E

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A

A

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|
Y

G

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A

A

E

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Y

T

C

G

E

E

P

S

S

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E

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A

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F

E

E

N

A

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S

A

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K

R

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E

E

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E

C

T

G

E

A

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T

I

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M

V

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H

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F

N

D

Q

D

E

Y

P

D

A

I

V

M

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

L

V

L

L

E

N

Q

Q

V

V

N

P

T

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I

V

D

D

T

A

I

L

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V

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P

I

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

V

I

G

T

A

V

K

K

S

A

V

L

N

K

P

P

D

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

A

P

K

S

A

N

A
|
A

P

D

A
x
D

M

C

H

Y

T

Q

A

S

Y

K

H

L

R

K

G

G

-

K

V

L

V

M

K

P

K

N

L

L

D

Y

K

P

V

P

S

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

Q

S

P

I

G

G

E

L

N
|
N

T

T

L

W

P

P

L

I

I

I

N

R

N

D

Y

L

V

V

D

D

I

I

I

F

T

T

V

V

S

T

E

E

E

D

E

E

I

I

A

K

D

C

A

A

I

T

V

Q

N

L

M

V

L

W

E

E

R

R

G

M

K

K

S

L

L

L

V

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

A

G

F

V

A

A

G

A

L

V

L

L

S

S

H

Q

N

H

D

F

Q

Q

I

T

D

V

S

S

-

P

-

E

-

V

R

K

H

N

C

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

F

V

D

D

active site: K53 (= K61), S76 (≠ A86), E202 (≠ Q212), A206 (= A216), D208 (≠ A218), G231 (= G240), L304 (≠ V311), S305 (= S312)
binding calcium ion: E202 (≠ Q212), A206 (= A216), D208 (≠ A218)
binding magnesium ion: N239 (= N249)
binding ortho-xylene: S76 (≠ A86), Q81 (= Q91), I96 (= I106), Y113 (= Y123)
binding pyridoxal-5'-phosphate: F52 (= F60), K53 (= K61), N78 (= N88), G177 (= G187), G178 (= G188), G179 (= G189), G180 (= G190), M181 (≠ L191), G231 (= G240), V232 (≠ I241), E275 (= E285), T277 (≠ A287), S305 (= S312), G306 (= G313)

Sites not aligning to the query:

binding magnesium ion: 3

Query Sequence

>WP_169315527.1 NCBI__GCF_000330705.1:WP_169315527.1
MIKESDLHGDFLTGGLVHDAWKRLDPVVHQTPIRTSATTNLRTGKNIYFKMENQQKTGAF
KFRGASYKLMRLSPKELDRGVITASAGNHAQGLALAAYKLGVKATIYMAEATPEAKVEAT
RGYGAEVVLTGESFQEAFEASLKQQERCGATYVHPFDDYDIMAGQGTIALELLEQVNTID
TIVVPIGGGGLISGIAVGAKSVNPDIKVIGVQAKAAPAMHTAYHRGVVKKLDKVSTIAEG
IAVKQPGENTLPLINNYVDDIITVSEEEIADAIVNMLERGKSLVEGAGAAAFAGLLSHND
QIDSRHCGVIVSGGNFDISRMAEIQSLANQLKPEQSHAALSF

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SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory