SitesBLAST

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
37% identity, 56% coverage: 33:325/519 of query aligns to 28:322/326 of 2gn2A

query
sites
2gn2A

M

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active site: K56 (= K58), A81 (= A83), Q207 (≠ E210), V211 (≠ A214), G213 (≠ S216), G235 (= G238), I308 (≠ N311), S309 (= S312)
binding cytidine-5'-monophosphate: R51 (≠ P53), T52 (≠ V54), G53 (≠ F55), A114 (= A116), D117 (≠ G119), Y118 (≠ Q120), N312 (= N315)

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)
36% identity, 51% coverage: 27:291/519 of query aligns to 37:299/339 of Q7XSN8

query
sites
Q7XSN8

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E219 (= E210) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ S216) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

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)
33% identity, 59% coverage: 18:324/519 of query aligns to 17:320/323 of O59791

query
sites
O59791

S

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K57 (= K58) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ A83) 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 (= N85) binding pyridoxal 5'-phosphate
G183 (= G185) binding pyridoxal 5'-phosphate
G184 (= G186) binding pyridoxal 5'-phosphate
G185 (= G187) binding pyridoxal 5'-phosphate
G186 (= G188) binding pyridoxal 5'-phosphate
L187 (= L189) binding pyridoxal 5'-phosphate
E208 (= E210) binding Mg(2+)
G212 (≠ A214) binding Mg(2+)
D214 (≠ S216) binding Mg(2+)
S308 (= S312) binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
33% identity, 59% coverage: 18:324/519 of query aligns to 12:315/318 of 1wtcA

query
sites
1wtcA

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active site: K52 (= K58), S77 (≠ A83), E203 (= E210), G207 (≠ A214), D209 (≠ S216), G231 (= G238), I302 (≠ A309), S303 (= S312)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ I26), K47 (≠ P53), M48 (≠ V54), A109 (≠ Q115), A110 (= A116), Y114 (≠ Q120)
binding magnesium ion: E203 (= E210), G207 (≠ A214), D209 (≠ S216)
binding pyridoxal-5'-phosphate: F51 (= F57), K52 (= K58), N79 (= N85), G178 (= G185), G179 (= G186), G180 (= G187), G181 (= G188), G231 (= G238), E276 (= E283), T278 (≠ S285), S303 (= S312)

1v71A Crystal structure of s.Pombe serine racemase
33% identity, 59% coverage: 18:324/519 of query aligns to 12:315/318 of 1v71A

query
sites
1v71A

S

S

A

E

P

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

S

T

P

P

L

V

D

L

P

T

M

S

P

S

R

T

L

V

S

N

L

K

R

E

L

F

G

V

T

A

P

E

V

V

R

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

Y

L

A

N

R

A

M

L

A

S

G

Q

L

L

P

N

R

E

E

A

A

Q

L

R

E

K

R

A

G

G

V

V

I

L

C

T

A

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

V

L

A

S

A

A

K

K

K

I

L

L

G

G

A

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

A

E

I

A

K

K

I

V

Q

A

A

A

V

T

K

K

G

G

Q

Y

G

G

R

Q

V

V

I

I

L

M

H

Y

G

D

E

R

S

Y

F

K

D

D

E

D

A

R

Y

E

S

K

H

M

A

A

Q

K

Q

E

L

I

E

S

A

E

E

R

K

E

G

G

L

L

T

T

F

I

I

I

H

P

P

P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

G

A

M

K

E

E

I

L

L

F

R

E

Q

E

H

-

P

V

D

G

P

P

L

L

E

D

A

A

I

L

F

F

V

V

P

C

I

L

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

V

L

Y

A

T

A

K

R

F

H

L

F

R

A

P

P

E

N

V

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

A

Q

A

S

L

F

A

R

A

K

G

G

D

S

R

I

V

V

I

H

L

I

N

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

R

Q

Q

H

A

L

G

G

E

N

E

Y

T

T

F

F

R

S

L

I

C

I

R

K

E

E

L

K

L

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

S
x
T

G

G

A

C

V

L

S

S

L

F

A

A

G

A

L

A

K

R

K

A

Y

M

V

K

E

E

R

K

E

L

G

K

A

N

R

K

Q

R

Q

I

G

G

L

I

V

I

A
x
I

V

-

N

-

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K52 (= K58), S77 (≠ A83), E203 (= E210), G207 (≠ A214), D209 (≠ S216), G231 (= G238), I302 (≠ A309), S303 (= S312)
binding magnesium ion: E203 (= E210), G207 (≠ A214), D209 (≠ S216)
binding pyridoxal-5'-phosphate: F51 (= F57), K52 (= K58), N79 (= N85), G178 (= G185), G179 (= G186), G180 (= G187), G181 (= G188), G231 (= G238), E276 (= E283), T278 (≠ S285), S303 (= S312), G304 (= G313)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
33% identity, 59% coverage: 18:324/519 of query aligns to 13:316/319 of 2zr8A

query
sites
2zr8A

S

S

A

E

P

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

S

T

P

P

L

V

D

L

P

T

M

S

P

S

R

T

L

V

S

N

L

K

R

E

L

F

G

V

T

A

P

E

V

V

R

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

Y

L

A

N

R

A

M

L

A

S

G

Q

L

L

P

N

R

E

E

A

A

Q

L

R

E

K

R

A

G

G

V

V

I

L

C

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

V

L

A

S

A

A

K

K

K

I

L

L

G

G

A

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

A

E

I

A

K

K

I

V

Q

A

A

A

V

T

K

K

G

G

Q

Y

G

G

R

Q

V

V

I

I

L

M

H

Y

G

D

E

R

S

Y

F

K

D

D

E

D

A
x
R

Y

E

S

K

H

M

A

A

Q

K

Q

E

L

I

E

S

A

E

E

R

K

E

G

G

L

L

T

T

F

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

G

A

M

K

E

E

I

L

L

F

R

E

Q

E

H

-

P

V

D

G

P

P

L

L

E

D

A

A

I

L

F

F

V

V

P

C

I

L

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

V

L

Y

A

T

A

K

R

F

H

L

F

R

A

P

P

E

N

V

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

A

Q

A

S

L

F

A

R

A

K

G

G

D

S

R

I

V

V

I

H

L

I

N

D

Q

T

V

P

G

K

L

T

F

I

A

A

D
|
D

G
|
G

V
x
A

A
x
Q

V
x
T

R

Q

Q

H

A

L

G

G

E

N

E

Y

T

T

F

F

R

S

L

I

C

I

R

K

E

E

L

K

L

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

S
x
T

G

G

A

C

V

L

S

S

L

F

A

A

G

A

L

A

K

R

K

A

Y

M

V

K

E

E

R

K

E

L

G

K

A

N

R

K

Q

R

Q

I

G

G

L

I

V

I

A
x
I

V

-

N

-

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K53 (= K58), S78 (≠ A83), E204 (= E210), G208 (≠ A214), D210 (≠ S216), G232 (= G238), I303 (≠ A309), S304 (= S312)
binding magnesium ion: E204 (= E210), G208 (≠ A214), D210 (≠ S216)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F57), K53 (= K58), S77 (= S82), S78 (≠ A83), N80 (= N85), H81 (= H86), P147 (= P152), G179 (= G185), G180 (= G186), G181 (= G187), G182 (= G188), G232 (= G238), E277 (= E283), T279 (≠ S285), S304 (= S312)
binding serine: S78 (≠ A83), R129 (≠ A134), D231 (= D237), G232 (= G238), A233 (≠ V239), Q234 (≠ A240), T235 (≠ V241)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
33% identity, 59% coverage: 18:324/519 of query aligns to 13:316/319 of 2zpuA

query
sites
2zpuA

S

S

A

E

P

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

S

T

P

P

L

V

D

L

P

T

M

S

P

S

R

T

L

V

S

N

L

K

R

E

L

F

G

V

T

A

P

E

V

V

R

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

Y

L

A

N

R

A

M

L

A

S

G

Q

L

L

P

N

R

E

E

A

A

Q

L

R

E

K

R

A

G

G

V

V

I

L

C

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

V

L

A

S

A

A

K

K

K

I

L

L

G

G

A

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

A

E

I

A

K

K

I

V

Q

A

A

A

V

T

K

K

G

G

Q

Y

G

G

R

Q

V

V

I

I

L

M

H

Y

G

D

E

R

S

Y

F

K

D

D

E

D

A

R

Y

E

S

K

H

M

A

A

Q

K

Q

E

L

I

E

S

A

E

E

R

K

E

G

G

L

L

T

T

F

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

G

A

M

K

E

E

I

L

L

F

R

E

Q

E

H

-

P

V

D

G

P

P

L

L

E

D

A

A

I

L

F

F

V

V

P

C

I

L

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

V

L

Y

A

T

A

K

R

F

H

L

F

R

A

P

P

E

N

V

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

A

Q

A

S

L

F

A

R

A

K

G

G

D

S

R

I

V

V

I

H

L

I

N

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

R

Q

Q

H

A

L

G

G

E

N

E

Y

T

T

F

F

R

S

L

I

C

I

R

K

E

E

L

K

L

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

S
x
T

G

G

A

C

V

L

S

S

L

F

A

A

G

A

L

A

K

R

K

A

Y

M

V

K

E

E

R

K

E

L

G

K

A

N

R

K

Q

R

Q

I

G

G

L

I

V

I

A
x
I

V

-

N

-

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K53 (= K58), S78 (≠ A83), E204 (= E210), G208 (≠ A214), D210 (≠ S216), G232 (= G238), I303 (≠ A309), S304 (= S312)
binding magnesium ion: E204 (= E210), G208 (≠ A214), D210 (≠ S216)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F57), K53 (= K58), S77 (= S82), S78 (≠ A83), N80 (= N85), H81 (= H86), P147 (= P152), G179 (= G185), G180 (= G186), G181 (= G187), G182 (= G188), G232 (= G238), E277 (= E283), T279 (≠ S285), 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)
33% identity, 57% coverage: 25:320/519 of query aligns to 20:312/319 of A4F2N8

query
sites
A4F2N8

A

A

I

N

E

R

S

T

P

P

L

V

D

F

P

T

M

S

P

R

R

T

L

L

S

D

L

A

R

E

L

T

G

G

T

A

P

Q

V

V

R

F

L

I

K

K

R

C

E

E

D

N

L

L

Q

Q

P

R

V

T

F

G

S

S

F

F

K
|
K

L

F

R

R

G

G

A

A

Y

F

A

N

R

A

M

L

A

S

G

R

L

F

P

D

R

E

E

A

A

Q

L

R

E

K

R

A

G

G

V

V

I

V

C

A

A

F

S

S

A

S

G

G

N

N

H

H

A

A

Q

Q

G

G

V

I

A

A

V

L

A

A

K

R

K

L

L

L

G

Q

A

M

K

P

A

A

T

T

I

I

V

V

M

M

P

P

R

T

T

D

T

A

P

P

A

A

I

A

K

K

I

V

Q

A

A

A

V

T

K

R

G

E

Q

Y

G

G

G

A

R

T

V

V

I

V

L

F

H

Y

G

D

E

R

S

I

F

T

D

E

E

D

A

R

Y

E

S

Q

H

I

A

G

Q

R

Q

T

L

L

E

A

A

E

E

Q

K

H

G

G

L

M

T

T

F

L

I

I

H

P

P

S

Y

Y

D

D

D

H

P

P

D

D

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

G

A

M

K

E

E

I

L

L

L

R

-

Q

E

H

F

P

T

D

G

P

P

L

L

E

D

A

A

I

L

F

F

V

V

P

G

I

L

G

G

L

M

A

L

A

S

G

G

V

T

A

A

V

L

Y

A

T

T

K

R

F

A

L

L

R

S

P

P

E

D

V

C

K

L

V

L

I

Y

G

G

V

V

E

E

P

P

E

E

D

A

A

G

A

N

S

D

M

G

A

Q

A

R

A

S

L

F

A

Q

A

T

G

G

D

S

R

I

V

V

I

H

L

I

N

D

Q

T

V

P

G

A

L

T

F

I

A

A

D

D

G

G

V

A

A

Q

V

T

R

Q

Q

H

A

L

G

G

E

N

E

H

T

T

F

F

R

P

L

I

C

I

R

R

E

E

L

N

L

V

D

N

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

A

E

E

I

L

C

V

A

E

A

S

V

M

K

R

D

F

I

F

F

M

E

Q

D

R

T

M

R

K

A

M

I

V

A

V

E

E

P

P

S

T

G

G

A

C

V

L

S

G

L

L

A

A

G

A

L

L

K

R

K

N

Y

L

V

K

E

Q

R

Q

E

F

G

R

A

G

R

Q

Q

R

Q

V

G

G

L

I

V

I

A

V

V

-

N

-

S

T

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

K

K53 (= K58) 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)
35% identity, 55% coverage: 46:329/519 of query aligns to 44:330/340 of Q9GZT4

query
sites
Q9GZT4

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P
x
K

V
x
T

F

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R
x
P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C
x
T

A

H

S

S

A

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q
x
Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

L

P

-

L

V

E
x
D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G

G

V

V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R
x
K

A

L

I

L

A

I

E

E

P

P

S

T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N

L

S
|
S

G

G

A

G

N
|
N

M

V

N

D

F

L

D

T

R

S

L

S

R

I

H

T

I

W

A

V

E

K

R

Q

A

A

E

E

K51 (≠ P53) binding ATP
T52 (≠ V54) binding ATP
K56 (= K58) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ R71) binding Ca(2+)
T81 (≠ C80) binding Ca(2+)
N86 (= N85) binding pyridoxal 5'-phosphate
Q89 (= Q88) binding ATP
Y121 (≠ Q120) binding ATP
D178 (≠ E178) binding Mg(2+)
G185 (= G185) binding pyridoxal 5'-phosphate
G186 (= G186) binding pyridoxal 5'-phosphate
G187 (= G187) binding pyridoxal 5'-phosphate
G188 (= G188) binding pyridoxal 5'-phosphate
M189 (≠ L189) binding pyridoxal 5'-phosphate
E210 (= E210) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (= A214) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ S216) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ E247) binding Ca(2+); binding Mg(2+)
K279 (≠ R279) binding ATP
S313 (= S312) binding pyridoxal 5'-phosphate
N316 (= N315) binding ATP

Sites not aligning to the query:

13 binding Mg(2+)
31 binding ATP
32 binding ATP
33 binding ATP

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/320 of 7nbhAAA

query
sites
7nbhAAA

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K
|
K

I

K

Q

L

A

A

V
x
I

K

Q

G

A

Q
x
Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G

G

L

M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D
|
D

G
|
G

V

V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P
|
P

S

T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G

G

A

G

N
|
N

M
x
V

N
x
D

F

L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A83), G85 (≠ A87), Q86 (= Q88), K111 (= K113), I115 (≠ V117), Y118 (≠ Q120), D235 (= D237), P281 (= P284), N313 (= N315), V314 (≠ M316), D315 (≠ N317)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/323 of 7nbfAAA

query
sites
7nbfAAA

L

F

K

K

R

C

E

E

D

L

L
x
F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q

Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding magnesium ion: N244 (≠ E247)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N83 (= N85), G182 (= G185), G183 (= G186), G184 (= G187), G185 (= G188), M186 (≠ L189), G236 (= G238), V237 (= V239), T282 (≠ S285), S310 (= S312), G311 (= G313)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: F46 (≠ L51)

Sites not aligning to the query:

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/323 of 7nbdAAA

query
sites
7nbdAAA

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q

Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F
x
W

E

E

D

R

T

M

R

K

A

L

I
x
L

A

I

E
|
E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M
x
V

N

D

F
x
L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F275), L278 (≠ I281), V314 (≠ M316), L316 (≠ F318)
binding magnesium ion: N244 (≠ E247)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N83 (= N85), G182 (= G185), G183 (= G186), G184 (= G187), G185 (= G188), M186 (≠ L189), G236 (= G238), V237 (= V239), E280 (= E283), T282 (≠ S285), 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)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/323 of 7nbcCCC

query
sites
7nbcCCC

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C
x
T

A
x
H

S

S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q

Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I
x
V

H
|
H

P
|
P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding biphenyl-4-ylacetic acid: T78 (≠ C80), H79 (≠ A81), H84 (= H86), V148 (≠ I150), H149 (= H151), P150 (= P152)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N83 (= N85), G182 (= G185), G183 (= G186), G184 (= G187), G185 (= G188), M186 (≠ L189), G236 (= G238), V237 (= V239), T282 (≠ S285), S310 (= S312), G311 (= G313)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/323 of 7nbcAAA

query
sites
7nbcAAA

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q

Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding magnesium ion: N244 (≠ E247)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N83 (= N85), G182 (= G185), G183 (= G186), G184 (= G187), G185 (= G188), M186 (≠ L189), G236 (= G238), V237 (= V239), T282 (≠ S285), S310 (= S312), G311 (= G313)

Sites not aligning to the query:

binding magnesium ion: 3

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 41:316/322 of 7nbgAAA

query
sites
7nbgAAA

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K
|
K

I

K

Q

L

A

A

V
x
I

K

Q

G

A

Q
x
Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K58), S81 (≠ A83), E207 (= E210), A211 (= A214), D213 (≠ S216), G236 (= G238), L309 (≠ N311), S310 (= S312)
binding calcium ion: E207 (= E210), A211 (= A214), D213 (≠ S216)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N83 (= N85), G182 (= G185), G183 (= G186), G184 (= G187), G185 (= G188), M186 (≠ L189), G236 (= G238), V237 (= V239), T282 (≠ S285), S310 (= S312), G311 (= G313)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A83), G85 (≠ A87), Q86 (= Q88), I101 (= I103), K111 (= K113), I115 (≠ V117), Y118 (≠ Q120)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
35% identity, 53% coverage: 46:318/519 of query aligns to 42:312/322 of 3l6bA

query
sites
3l6bA

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

R

E

K

A

-

L

-

E

P

R

K

G

A

V

V

I

V

C

T

A

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q

Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y
x
R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E
|
E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K54 (= K58), S77 (≠ A83), E203 (= E210), A207 (= A214), D209 (≠ S216), G232 (= G238), T278 (≠ S285), L305 (≠ N311), S306 (= S312)
binding malonate ion: K54 (= K58), S76 (= S82), S77 (≠ A83), N79 (= N85), H80 (= H86), R128 (≠ Y135), G232 (= G238)
binding manganese (ii) ion: E203 (= E210), A207 (= A214), D209 (≠ S216)
binding pyridoxal-5'-phosphate: F53 (= F57), K54 (= K58), N79 (= N85), G178 (= G185), G179 (= G186), G180 (= G187), G181 (= G188), M182 (≠ L189), V233 (= V239), E276 (= E283), T278 (≠ S285), S306 (= S312), G307 (= G313)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 52% coverage: 46:317/519 of query aligns to 41:310/310 of 7nbgDDD

query
sites
7nbgDDD

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

Y

L

A

N

R

A

M

V

A

R

G

S

L

L

P

V

R

R

E

K

A

P

L

-

E

-

R

K

G

A

V

V

I

V

C

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

V

Y

A

A

K

K

K

L

L

E

G

G

A

I

K

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

A

D

I

C

K

K

I

K

Q

L

A

A

V

I

K

Q

G

A

Q
x
Y

G

G

G

A

R

S

V

-

I

I

L

V

H

Y

G

C

E

E

S

P

F

S

D

D

E

E

A

S

Y

R

S

E

H

N

-

V

A

A

Q

K

Q

R

L

V

E

T

A

E

E

E

K

T

G

E

L

G

T

I

F

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

P

P

D

-

P

L

L

V

E

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

V

I

Y

T

T

V

K

K

F

A

L

L

R

K

P

P

E

S

V

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

A

Y

A

Q

A

S

L

K

A

L

A

K

G

G

D

K

R

L

V

M

-

P

I

N

L

L

N

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

R

S

Q

S

A

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

R

R

E

D

L

L

L

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E
|
E

P

P

S
x
T

G

A

A

G

V

V

S

G

L

V

A

A

G

A

-

V

L

L

K

S

K

Q

Y

H

V

F

E

Q

R

T

E

V

G

S

A

P

R

E

Q

V

Q

K

G

N

L

I

V

C

A

I

V

V

N
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

active site: K53 (= K58), S76 (≠ A83), E202 (= E210), A206 (= A214), D208 (≠ S216), G231 (= G238), L304 (≠ N311), S305 (= S312)
binding calcium ion: E202 (= E210), A206 (= A214), D208 (≠ S216)
binding magnesium ion: N239 (≠ E247)
binding ortho-xylene: S76 (≠ A83), Q81 (= Q88), I96 (= I103), Y113 (≠ Q120)
binding pyridoxal-5'-phosphate: F52 (= F57), K53 (= K58), N78 (= N85), G177 (= G185), G178 (= G186), G179 (= G187), G180 (= G188), M181 (≠ L189), G231 (= G238), V232 (= V239), E275 (= E283), T277 (≠ S285), S305 (= S312), G306 (= G313)

Sites not aligning to the query:

binding magnesium ion: 3

Query Sequence

>WP_085985190.1 NCBI__GCF_000262405.1:WP_085985190.1
MNQEGGSDVQDYIRRILSAPVYDVAIESPLDPMPRLSLRLGTPVRLKREDLQPVFSFKLR
GAYARMAGLPREALERGVICASAGNHAQGVAVAAKKLGAKATIVMPRTTPAIKIQAVKGQ
GGRVILHGESFDEAYSHAQQLEAEKGLTFIHPYDDPDVIAGQGTVGMEILRQHPDPLEAI
FVPIGGGGLAAGVAVYTKFLRPEVKVIGVEPEDAASMAAALAAGDRVILNQVGLFADGVA
VRQAGEETFRLCRELLDEVITVSTDEICAAVKDIFEDTRAIAEPSGAVSLAGLKKYVERE
GARQQGLVAVNSGANMNFDRLRHIAERAELGEHREALLAVTIPEQPGSYRRFIQLLGKRS
ITEFNYRYSDPQEAQIFVGVQLSDGDPEKRQIIAMLREQGYPVLDMSDNEMAKLHVRYMV
GGHTPGLQDELIFRFQFPERPGALLKFLNGLSGSWNISLFHYRNHGADYGRVLAGIQVPT
AERAQLKHSLDELGYPYWDESDNPAYRSFLNRGKEGATT

Or try a new SitesBLAST search

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