SitesBLAST

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)
37% identity, 97% coverage: 9:330/331 of query aligns to 7:322/323 of O59791

query
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O59791

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K57 (= K59) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S84) 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 (= N86) binding pyridoxal 5'-phosphate
G183 (≠ S190) binding pyridoxal 5'-phosphate
G184 (= G191) binding pyridoxal 5'-phosphate
G185 (= G192) binding pyridoxal 5'-phosphate
G186 (= G193) binding pyridoxal 5'-phosphate
L187 (= L194) binding pyridoxal 5'-phosphate
E208 (= E215) binding Mg(2+)
G212 (≠ F219) binding Mg(2+)
D214 (= D221) binding Mg(2+)
S308 (= S316) binding pyridoxal 5'-phosphate

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
37% identity, 97% coverage: 9:330/331 of query aligns to 3:318/319 of 2zr8A

query
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2zr8A

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active site: K53 (= K59), S78 (= S84), E204 (= E215), G208 (≠ F219), D210 (= D221), G232 (≠ A244), I303 (≠ L315), S304 (= S316)
binding magnesium ion: E204 (= E215), G208 (≠ F219), D210 (= D221)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F58), K53 (= K59), S77 (= S83), S78 (= S84), N80 (= N86), H81 (= H87), P147 (= P153), G179 (≠ S190), G180 (= G191), G181 (= G192), G182 (= G193), G232 (≠ A244), E277 (= E289), T279 (≠ G291), S304 (= S316)
binding serine: S78 (= S84), R129 (= R135), D231 (= D243), G232 (≠ A244), A233 (≠ L245), Q234 (≠ M246), T235 (≠ V247)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
37% identity, 97% coverage: 9:330/331 of query aligns to 3:318/319 of 2zpuA

query
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2zpuA

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active site: K53 (= K59), S78 (= S84), E204 (= E215), G208 (≠ F219), D210 (= D221), G232 (≠ A244), I303 (≠ L315), S304 (= S316)
binding magnesium ion: E204 (= E215), G208 (≠ F219), D210 (= D221)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F58), K53 (= K59), S77 (= S83), S78 (= S84), N80 (= N86), H81 (= H87), P147 (= P153), G179 (≠ S190), G180 (= G191), G181 (= G192), G182 (= G193), G232 (≠ A244), E277 (= E289), T279 (≠ G291), S304 (= S316)

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)
37% identity, 95% coverage: 15:329/331 of query aligns to 24:336/339 of Q7XSN8

query
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Q7XSN8

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N

T

D

L

S

P

S

S

T

T

G

N

S

T

A

I

C

A

D

D

A

G

L

L

M

R

V

A

Q

F

T

L

P

-

G

G

D

D

I

L

T

T

L

W

A

P

L

V

A

V

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

I

A

V

V

V

S

D

D

D

G

N

E

A

A

I

F

V

A

D

A

A

M

M

R

K

F

M

A

C

F

Y

D

E

H

M

L

L

K

K

L

V

V

A

V

V

E

E

P

P

G

S

G

G

A

A

V

I

A

G

L

L

A

A

L

A

L

L

S

S

G

D

R

E

L

F

P

K

V

Q

A

S

-

S

-

A

-

W

-

H

-

E

G

S

R

S

T

K

V

I

A

G

V

I

L

V

S

S

G

G

N

N

V

V

D

D

A

L

A

G

L

V

F

L

A

W

R

E

V

S

L

L

E219 (= E215) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D221) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

5cvcA Structure of maize serine racemase (see paper)
37% identity, 94% coverage: 12:321/331 of query aligns to 2:312/329 of 5cvcA

query
sites
5cvcA

A

A

D

D

V

I

E

D

-

S

-

I

-

R

D

E

A

A

A

Q

R

A

R

R

L

I

A

A

G

P

Q

Y

A

V

V

H

V

R

T

T

P

P

L

V

L

M

R

S

H

S

A

T

E

S

L

I

D

D

R

A

L

M

T

V

G

G

A

K

T

K

V

L

L

F

V

F

K

K

P

C

E

E

V

C

L

F

Q

Q

V

K

T

A

G

G

S

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

S

N

N

R

S

L

I

S

F

R

A

I

L

P

D

A

D

A

E

E

Q

R

V

S

S

R

K

G

G

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

A

G

A

V

V

A

A

E

L

A

A

R

K

R

L

L

R

G

G

M

I

P

P

A

A

T

H

I

I

V

V

M

I

P

P

A

R

D

N

A

A

P

P

A

A

R

S

K

K

I

V

A

E

N

N

T

V

R

K

A

C

L

Y

G

G

V

G

S

H

V

I

L

W

Y

S

D

D

R

A

A

S

T

I

E

E

S

S

R

R

E

E

A

Y

I

V

G

S

G

K

R

R

I

V

A

Q

A

E

E

E

R

T

G

G

A

A

T

V

I

L

V

I

P

H

P

P

F

I

D

N

D

S

V

K

H

Y

I

T

I

I

A

S

G

G

Q

Q

G

G

T

T

V

V

G

S

L

L

E

E

I

L

G

L

R

E

Q

Q

A

V

R

P

E

E

L

-

G

-

V

-

A

-

V

I

D

D

H

T

C

I

L

I

V

V

C

P

C

I

S
|
S

G
|
G

L

L

A

I

T

S

G

G

T

V

A

A

L

L

G

A

L

A

H

K

L

A

S

I

H

N

P

P

G

S

A

I

R

R

V

I

H

L

T

A

V

A

E
|
E

P

P

V

K

G

G

F
x
A

D

D

D
|
D

F

S

A

A

R

Q

S

S

L

K

A

A

S

A

G

G

R

-

K

K

E

I

R

I

N

T

D

L

S

P

S

S

T

T

G

N

S

T

A

I

C

A

D

D

A
x
G

L
|
L

M

R

V

A

Q

F

T

L

P

-

G

G

D

D

I

L

T

T

L

W

A

P

L

V

A

V

R

R

R

D

E

L

L

V

A

D

E

D

G

V

L

I

A

V

V

V

S

D

D

D

G

T

E

A

A

I

F

V

A

D

A

A

M

M

R

K

F

M

A

C

F

Y

D

E

H

I

L

L

K

K

L

V

V

A

V

V

E
|
E

P

P

G

S

G

G

A

A

V

I

A

G

L

L

A

A

L

A

L

L

S

S

G

D

R

E

L

F

P

K

V

Q

A

S

-

S

-

A

-

W

-

H

-

E

G

S

R

S

T

K

V

I

A

G

V

I

L
x
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K52 (= K59), S77 (= S84), E203 (= E215), A207 (≠ F219), D209 (= D221), G231 (≠ A244), V306 (≠ L315), S307 (= S316)
binding magnesium ion: E203 (= E215), A207 (≠ F219), D209 (= D221)
binding pyridoxal-5'-phosphate: F51 (= F58), K52 (= K59), N79 (= N86), S178 (= S190), G179 (= G191), G180 (= G192), G181 (= G193), L232 (= L245), E275 (= E289), S307 (= S316), G308 (= G317)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/322 of 7nbgAAA

query
sites
7nbgAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K
|
K

I

K

A

L

N

A

T
x
I

R

Q

A

A

L
x
Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N83 (= N86), G182 (≠ S190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (≠ A244), V237 (≠ L245), T282 (≠ G291), S310 (= S316), G311 (= G317)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (= S84), G85 (≠ A88), Q86 (= Q89), I101 (= I104), K111 (= K114), I115 (≠ T118), Y118 (≠ L121)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/323 of 7nbfAAA

query
sites
7nbfAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V
x
H

V
x
L

T
|
T

P
|
P

L

V

L
|
L

R
x
T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L
x
F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I
x
N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding magnesium ion: N244 (≠ I253)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N83 (= N86), G182 (≠ S190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (≠ A244), V237 (≠ L245), T282 (≠ G291), S310 (= S316), G311 (= G317)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ V27), L22 (≠ V28), T23 (= T29), P24 (= P30), L26 (= L32), T27 (≠ R33), F46 (≠ L52)

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)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/323 of 7nbdAAA

query
sites
7nbdAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I
x
N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F
x
W

D

E

H

R

L

M

K

K

L

L

V
x
L

V

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V
|
V

D

D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F281), L278 (≠ V287), V314 (= V320)
binding magnesium ion: N244 (≠ I253)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N83 (= N86), G182 (≠ S190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (≠ A244), V237 (≠ L245), E280 (= E289), T282 (≠ G291), S310 (= S316), G311 (= G317)

Sites not aligning to the query:

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/323 of 7nbcCCC

query
sites
7nbcCCC

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A
x
T

W
x
H

S

S

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V
|
V

P
x
H

P
|
P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding biphenyl-4-ylacetic acid: T78 (≠ A81), H79 (≠ W82), H84 (= H87), V148 (= V151), H149 (≠ P152), P150 (= P153)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N83 (= N86), G182 (≠ S190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (≠ A244), V237 (≠ L245), T282 (≠ G291), S310 (= S316), G311 (= G317)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/323 of 7nbcAAA

query
sites
7nbcAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I
x
N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding magnesium ion: N244 (≠ I253)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N83 (= N86), G182 (≠ S190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (≠ A244), V237 (≠ L245), T282 (≠ G291), S310 (= S316), G311 (= G317)

Sites not aligning to the query:

binding magnesium ion: 3

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
35% identity, 93% coverage: 13:321/331 of query aligns to 7:315/320 of 7nbhAAA

query
sites
7nbhAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F

F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P

P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K
|
K

I

K

A

L

N

A

T
x
I

R

Q

A

A

L
x
Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S

G

G

G

L

M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D
|
D

A
x
G

L

V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P
|
P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G

G

N
|
N

V
|
V

D
|
D

active site: K53 (= K59), S81 (= S84), E207 (= E215), A211 (≠ F219), D213 (= D221), G236 (≠ A244), L309 (= L315), S310 (= S316)
binding calcium ion: E207 (= E215), A211 (≠ F219), D213 (= D221)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (= S84), G85 (≠ A88), Q86 (= Q89), K111 (= K114), I115 (≠ T118), Y118 (≠ L121), D235 (= D243), P281 (= P290), N313 (= N319), V314 (= V320), D315 (= D321)

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, 93% coverage: 13:321/331 of query aligns to 10:318/340 of Q9GZT4

query
sites
Q9GZT4

A

A

D

D

V

V

E
|
E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H
x
S

A
x
S

E
x
I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V
x
K

T
|
T

G

G

S

S

F

F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

-

R

S

S

R

L

I

V

P
|
P

A

D

A

A

-

L

-

E

E

R

R

K

S

P

R

K

G

A

V

V

A
x
T

W

H

S

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L
x
Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D
|
D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A

G

L

V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I
x
N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K
|
K

L

L

V

L

V

I

E

E

P

P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L

L

S
|
S

G

G

N
|
N

V

V

D

D

E13 (= E16) binding Mg(2+)
S31 (≠ H34) binding ATP
S32 (≠ A35) binding ATP
I33 (≠ E36) binding ATP
K51 (≠ V54) binding ATP
T52 (= T55) binding ATP
K56 (= K59) modified: N6-(pyridoxal phosphate)lysine
P69 (= P71) binding Ca(2+)
T81 (≠ A81) binding Ca(2+)
N86 (= N86) binding pyridoxal 5'-phosphate
Q89 (= Q89) binding ATP
Y121 (≠ L121) binding ATP
D178 (= D183) binding Mg(2+)
G185 (≠ S190) binding pyridoxal 5'-phosphate
G186 (= G191) binding pyridoxal 5'-phosphate
G187 (= G192) binding pyridoxal 5'-phosphate
G188 (= G193) binding pyridoxal 5'-phosphate
M189 (≠ L194) binding pyridoxal 5'-phosphate
E210 (= E215) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ F219) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (= D221) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ I253) binding Ca(2+); binding Mg(2+)
K279 (= K285) binding ATP
S313 (= S316) binding pyridoxal 5'-phosphate
N316 (= N319) binding ATP

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
34% identity, 93% coverage: 13:321/331 of query aligns to 7:310/310 of 7nbgDDD

query
sites
7nbgDDD

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

S

R

R

S

I

L

P

-

A

-

A

V

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L
x
Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I
x
N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K59), S76 (= S84), E202 (= E215), A206 (≠ F219), D208 (= D221), G231 (≠ A244), L304 (= L315), S305 (= S316)
binding calcium ion: E202 (= E215), A206 (≠ F219), D208 (= D221)
binding magnesium ion: N239 (≠ I253)
binding ortho-xylene: S76 (= S84), Q81 (= Q89), I96 (= I104), Y113 (≠ L121)
binding pyridoxal-5'-phosphate: F52 (= F58), K53 (= K59), N78 (= N86), G177 (≠ S190), G178 (= G191), G179 (= G192), G180 (= G193), M181 (≠ L194), G231 (≠ A244), V232 (≠ L245), E275 (= E289), T277 (≠ G291), S305 (= S316), G306 (= G317)

Sites not aligning to the query:

binding magnesium ion: 3

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
34% identity, 93% coverage: 13:321/331 of query aligns to 8:311/322 of 3l6bA

query
sites
3l6bA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

S

R

R

S

I

L

P

-

A

-

A

V

E

R

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R
|
R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S
x
G

G
|
G

L
x
M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L
x
V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D

E

H

R

L

M

K

K

L

L

V

L

V

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K54 (= K59), S77 (= S84), E203 (= E215), A207 (≠ F219), D209 (= D221), G232 (≠ A244), T278 (≠ G291), L305 (= L315), S306 (= S316)
binding malonate ion: K54 (= K59), S76 (= S83), S77 (= S84), N79 (= N86), H80 (= H87), R128 (= R135), G232 (≠ A244)
binding manganese (ii) ion: E203 (= E215), A207 (≠ F219), D209 (= D221)
binding pyridoxal-5'-phosphate: F53 (= F58), K54 (= K59), N79 (= N86), G178 (≠ S190), G179 (= G191), G180 (= G192), G181 (= G193), M182 (≠ L194), V233 (≠ L245), E276 (= E289), T278 (≠ G291), S306 (= S316), G307 (= G317)

6zspAAA serine racemase bound to atp and malonate. (see paper)
34% identity, 93% coverage: 13:321/331 of query aligns to 7:308/320 of 6zspAAA

query
sites
6zspAAA

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H
x
S

A
x
S

E
x
I

L

L

D

N

R

Q

L

L

T

T

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V
x
K

T
|
T

G

G

S

S

F

F

K
|
K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

V

S

R

R

S

I

L

P

-

A

-

E

-

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

D

R

C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L
x
Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

E

R

P

A

S

T

D

E

E

S

S

R
|
R

E

E

A

N

I

V

G

A

G

K

R

R

I

V

A

T

A

E

E

E

R

T

G

E

A

G

T

I

I

M

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S

G

G

G

L

M

A

L

T

A

G

G

T

I

A

A

L

I

G

T

L

V

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E
|
E

P

P

V

S

G

N

F
x
A

D

D

D
|
D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

K

K

L

E

M

R

P

N

N

D

L

S

Y

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A
x
G

L

V

M

K

V

-

Q
x
S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

I

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

C

A

A

M

T

R

Q

F

L

A

V

F

W

D
x
E

H
x
R

L

M

K
|
K

L

L

V

L

V

I

E

E

P

P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

I

A

C

V

I

V

V

L
|
L

S
|
S

G

G

N
|
N

V

V

D

D

active site: K53 (= K59), S74 (= S84), E200 (= E215), A204 (≠ F219), D206 (= D221), G229 (≠ A244), L302 (= L315), S303 (= S316)
binding adenosine-5'-triphosphate: S28 (≠ H34), S29 (≠ A35), I30 (≠ E36), K48 (≠ V54), T49 (= T55), Q79 (= Q89), Y111 (≠ L121), E266 (≠ D282), R267 (≠ H283), K269 (= K285), N306 (= N319)
binding magnesium ion: E200 (= E215), A204 (≠ F219), D206 (= D221)
binding malonate ion: K53 (= K59), S73 (= S83), S74 (= S84), N76 (= N86), H77 (= H87), R125 (= R135), G229 (≠ A244), S232 (≠ Q248)

8y1jA Structure of the pyridoxal 5'-phosphate-dependent (plp) threonine deaminase ilva1 from pseudomonas aeruginosa pao1 (see paper)
36% identity, 91% coverage: 21:321/331 of query aligns to 12:309/502 of 8y1jA

query
sites
8y1jA

R

R

L

V

A

Y

G

D

Q

V

A

A

V

V

V

E

T

T

P

P

L

L

L

Q

R

P

H

A

A

R

E

Q

L

L

D

S

R

E

L

R

T

L

G

G

A

N

T

Q

V

V

L

L

V

L

K

K

P

R

E

E

V

D

L

L

Q

Q

V

P

T

V

G

F

S

S

F

F

K
|
K

F

I

R

R

G

G

A

A

F

Y

N

N

R

K

L

V

S

A

R

Q

I

L

P

T

A

E

E

E

R

K

S

A

R

R

G

G

V

V

V

I

A

A

W

A

S
|
S

S

A

G

G

N

N

H
|
H

A

A

Q

Q

G

G

V

L

A

A

E

L

A

A

R

K

R

R

L

Q

G

G

M

I

P

R

A

A

T

V

I

I

V

V

M

M

P

P

A

K

D

T

A

T

P

P

A

E

R

I

K

K

I

V

A

Q

N

A

T

V

R

R

A

A

L

H

G

G

V

A

S

K

V

A

V

V

L

L

Y

H

D

G

R

D

A

A

T

F

E

P

S

E

R

A

E

L

A

A

I

H

G

A

G

L

R

K

I

L

A

V

A

D

E

E

R

K

G

G

A

Y

T

T

I

F

V

V

P

H

P

P

F

Y

D

D

V

P

H

D

I

T

I

I

A

A

G

G

Q

Q

G

G

T

T

V

V

G

A

L

M

E

E

I

I

G

L

R

R

Q

Q

A

Q

R

P

E

-

L

-

G

-

V

-

A

G

A

R

V

L

D

D

H

A

C

I

L

F

V

V

C

P

C

V

S

G

G

G

L

L

A

V

T

A

G

G

T

I

A

A

L

A

G

Y

L

V

H

K

L

Y

S

L

H

R

P

P

G

E

A

I

R

K

V

V

H

I

T

G

V

V

E

E

P

P

V

D

G

E

F

S

D

N

D

C

F

L

A

Q

R

A

S

A

L

M

A

A

S

A

G

G

R

E

K

R

E

V

R

V

N

L

D

-

S

G

S

Q

T

V

G

G

S

L

A

F

C

A

D

D

A

G

L

V

M

A

V

V

Q

A

T

Q

P

I

G

G

D

Q

I

H

T

T

L

F

A

D

L

I

A

C

R

K

R

D

E

H

L

V

A

D

E

E

G

V

L

I

A

T

V

V

S

S

D

T

G

D

E

E

A

I

F

C

A

A

M

I

R

K

F

D

A

I

F

Y

D

D

H

D

L

T

K

R

L

S

V

I

V

T

E

E

P

P

G

A

G

G

A

A

V

L

A

A

L

V

A

A

A

G

L

I

-

K

L

Y

S

V

G

E

R

R

L

E

P

R

V

A

A

E

G

G

R

Q

T

T

V

L

A

V

V

A

V

I

L

D

S

S

G

G

G

A

N

N

V

V

D

N

binding 2-ketobutyric acid: K50 (= K59), S74 (= S83), H78 (= H87)

Sites not aligning to the query:

binding 2-ketobutyric acid: 336, 337, 338, 340, 341, 358, 448, 449

Q9QZX7 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 Mus musculus (Mouse) (see paper)
36% identity, 93% coverage: 13:321/331 of query aligns to 10:318/339 of Q9QZX7

query
sites
Q9QZX7

A

A

D

D

V

V

E

E

D

K

A

A

A

H

R

I

R

N

L

I

A

Q

G

D

Q

S

A

I

V

H

V

L

T

T

P

P

L

V

L

L

R

T

H

S

A

S

E

I

L

L

D

N

R

Q

L

I

T

A

G

G

A

R

T

N

V

L

L

F

V

F

K

K

P

C

E

E

V

L

L

F

Q

Q

V

K

T

T

G

G

S

S

F

F

K

K

F

I

R

R

G

G

A

A

F

L

N

N

R

A

L

I

S

R

-

G

R

L

I

I

P

P

-

D

-

T

A

P

A

E

E

E

R

K

S

P

R

K

G

A

V

V

A

T

W

H

S

S

G

G

N

N

H

H

A

G

Q

Q

G

A

V

L

A

T

E

Y

A

A

R

K

R

L

L

E

G

G

M

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

A

Q

D

T

A

A

P

P

A

N

R
x
C

K

K

I

K

A

L

N

A

T

I

R

Q

A

A

L

Y

G

G

V

A

S

S

V

I

V

V

L

Y

Y

C

D

D

R

P

A

S

T

D

E

E

S

S

R

R

E

E

A

K

I

V

G

T

G

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R

R

I

I

A

M

A

Q

E

E

R

T

G

E

A

G

T

I

I

L

V

V

P

H

P

P

F

N

D

Q

D

E

V

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

G

L

R

N

Q

Q

A

-

R

-

E

-

L

-

G

-

V

V

A

P

A

L

V

V

D

D

H

A

C

L

L

V

V

V

C

P

C

V

S

G

G

G

L

M

A

V

T

A

G

G

T

I

A

A

L

I

G

T

L

I

H

K

L

A

S

L

H

K

P

P

G

S

A

V

R

K

V

V

H

Y

T

A

V

A

E

E

P

P

V

S

G

N

F

A

D

D

F

C

A

Y

R

Q

S

S

L

K

A

L

S

K

G

G

R

E

K

L

E

T

R

P

N

N

D

L

S

H

S

P

T

P

G

E

S

T

A

I

C

A

D

D

A

G

L

V

M

K

V

-

Q

S

T

S

P

I

G

G

D

L

I

N

T

T

L

W

A

P

L

I

A

I

R

R

R

D

E

L

L

V

A

D

E

D

G

V

L

F

A

T

V

V

S

T

D

E

G

D

E

E

A

I

F

K

A

Y

A

A

M

T

R

Q

F

L

A

V

F

W

D

G

H

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G

T

G

A

A

G

V

V

A

A

L

L

A

A

L

V

L

L

S

S

G

Q

R

H

L

F

P

Q

V

T

A

V

G

S

-

P

-

E

-

V

R

K

T

N

V

V

A

C

V

I

V

V

L

L

S

S

G

G

N

N

V

V

D

D

C113 (≠ R113) modified: S-nitrosocysteine; mutation to S: Abolishes S-nitrosylation.

Query Sequence

>WP_012566001.1 NCBI__GCF_000016185.1:WP_012566001.1
MDAAALPTLPTAADVEDAARRLAGQAVVTPLLRHAELDRLTGATVLVKPEVLQVTGSFKF
RGAFNRLSRIPAAERSRGVVAWSSGNHAQGVAEAARRLGMPATIVMPADAPARKIANTRA
LGVSVVLYDRATESREAIGGRIAAERGATIVPPFDDVHIIAGQGTVGLEIGRQARELGVA
AVDHCLVCCSGGGLATGTALGLHLSHPGARVHTVEPVGFDDFARSLASGRKERNDSSTGS
ACDALMVQTPGDITLALARRELAEGLAVSDGEAFAAMRFAFDHLKLVVEPGGAVALAALL
SGRLPVAGRTVAVVLSGGNVDAALFARVLAG

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