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)
38% identity, 95% coverage: 7:319/330 of query aligns to 8:321/323 of O59791

query
sites
O59791

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K57 (= K52) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S77) 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 (= N79) binding pyridoxal 5'-phosphate
G183 (= G183) binding pyridoxal 5'-phosphate
G184 (= G184) binding pyridoxal 5'-phosphate
G185 (= G185) binding pyridoxal 5'-phosphate
G186 (= G186) binding pyridoxal 5'-phosphate
L187 (= L187) binding pyridoxal 5'-phosphate
E208 (= E204) binding Mg(2+)
G212 (≠ W208) binding Mg(2+)
D214 (= D210) binding Mg(2+)
S308 (= S306) binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
38% identity, 95% coverage: 7:319/330 of query aligns to 3:316/318 of 1wtcA

query
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1wtcA

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active site: K52 (= K52), S77 (= S77), E203 (= E204), G207 (≠ W208), D209 (= D210), G231 (≠ A234), I302 (≠ V305), S303 (= S306)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ T24), K47 (≠ Q47), M48 (≠ G48), A109 (≠ D109), A110 (= A110), Y114 (≠ A114)
binding magnesium ion: E203 (= E204), G207 (≠ W208), D209 (= D210)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), G178 (= G183), G179 (= G184), G180 (= G185), G181 (= G186), G231 (≠ A234), E276 (= E279), T278 (≠ G281), S303 (= S306)

1v71A Crystal structure of s.Pombe serine racemase
38% identity, 95% coverage: 7:319/330 of query aligns to 3:316/318 of 1v71A

query
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1v71A

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active site: K52 (= K52), S77 (= S77), E203 (= E204), G207 (≠ W208), D209 (= D210), G231 (≠ A234), I302 (≠ V305), S303 (= S306)
binding magnesium ion: E203 (= E204), G207 (≠ W208), D209 (= D210)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), G178 (= G183), G179 (= G184), G180 (= G185), G181 (= G186), G231 (≠ A234), E276 (= E279), T278 (≠ G281), S303 (= S306), G304 (= G307)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
38% identity, 95% coverage: 7:319/330 of query aligns to 4:317/319 of 2zr8A

query
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2zr8A

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G

L
x
A

Q
|
Q

T
|
T

T

Q

R

H

V

L

S

G

P

N

L

Y

T

T

F

F

E

S

A

I

L

I

R

K

D

E

A

K

G

V

A

D

R

D

G

I

V

L

A

T

V

V

S

S

E

D

G

E

E

E

V

L

Q

I

A

D

A

C

M

L

A

K

F

F

A

Y

A

A

R

A

H

R

L

M

R

K

L

I

V

V

A

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

A

S

L

F

A

A

L

R

S

A

G

M

R

K

A

E

G

K

P

L

L

K

P

N

A

K

R

R

T

I

A

G

I

I

L

I

V
x
I

S
|
S

G

G

N

N

V

V

D

D

P

I

A

E

F

R

Y

Y

A

A

E

H

V

F

I

L

active site: K53 (= K52), S78 (= S77), E204 (= E204), G208 (≠ W208), D210 (= D210), G232 (≠ A234), I303 (≠ V305), S304 (= S306)
binding magnesium ion: E204 (= E204), G208 (≠ W208), D210 (= D210)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F51), K53 (= K52), S77 (= S76), S78 (= S77), N80 (= N79), H81 (= H80), P147 (≠ S146), G179 (= G183), G180 (= G184), G181 (= G185), G182 (= G186), G232 (≠ A234), E277 (= E279), T279 (≠ G281), S304 (= S306)
binding serine: S78 (= S77), R129 (= R128), D231 (= D233), G232 (≠ A234), A233 (≠ L235), Q234 (= Q236), T235 (= T237)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
38% identity, 95% coverage: 7:319/330 of query aligns to 4:317/319 of 2zpuA

query
sites
2zpuA

P

P

Q

T

R

Y

A

D

G

D

V

V

V

A

A

S

A

A

A

S

E

E

R

R

L

I

R

K

G

K

H

F

V

A

T

N

E

K

T

T

P

P

L

V

L

L

P

T

L

S

A

S

W

T

Q

V

G

N

R

K

R

E

L

F

-

V

-

A

-

E

-

V

W

F

I

F

K

K

A

C

E

E

C

N

L

F

Q

Q

Q

K

G

M

G

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

M

L

N

N

R

A

L

L

L

S

Q

Q

L

L

D

N

D

E

A

A

Q

Q

K

R

A

K

A

A

G

G

V

V

V

L

A

T

F

F

S
|
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

R

K

Q

I

L

L

G

G

I

I

A

P

A

A

T

K

I

I

V

I

M

M

P

P

H

L

D

D

A

A

P

P

A

E

V

A

K

K

R

V

D

A

A

A

T

T

L

K

A

G

A

Y

G

G

A

G

S

Q

V

V

V

I

G

M

Y

Y

D

D

R

R

L

Y

R

K

E

D

S

D

R

R

E

E

S

K

I

M

G

A

A

K

R

E

L

I

A

S

E

E

E

R

R

E

G

G

A

L

V

T

L

I

V

I

P

P

S
x
P

F

Y

D

D

D

H

V

P

D

H

V

V

I

L

E

A

G

G

Q

Q

G

G

S

T

A

A

G

A

V

K

E

E

I

L

G

F

R

E

Q

E

M

V

A

-

L

-

A

-

D

-

G

G

P

P

P

L

E

D

M

A

V

L

L

F

V

V

C

C

C

L

G
|
G

L

L

S

L

A

S

G

G

I

S

A

A

L

L

A

A

L

A

-

R

-

H

-

F

-

A

P

P

D

N

A

C

E

E

I

V

V

Y

T

G

V

V

E
|
E

P

P

E

E

G

A

W
x
G

D

N

D
|
D

M

G

A

Q

Q

Q

S

S

L

F

A

R

S

K

G

G

A

S

I

I

V

V

E

H

V

I

G

-

K

-

D

D

A

T

P

P

P

K

T

T

R

I

C

A

D

D

A
x
G

L

A

Q

Q

T

T

T

Q

R

H

V

L

S

G

P

N

L

Y

T

T

F

F

E

S

A

I

L

I

R

K

D

E

A

K

G

V

A

D

R

D

G

I

V

L

A

T

V

V

S

S

E

D

G

E

E

E

V

L

Q

I

A

D

A

C

M

L

A

K

F

F

A

Y

A

A

R

A

H

R

L

M

R

K

L

I

V

V

A

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

A

S

L

F

A

A

L

R

S

A

G

M

R

K

A

E

G

K

P

L

L

K

P

N

A

K

R

R

T

I

A

G

I

I

L

I

V
x
I

S
|
S

G

G

N

N

V

V

D

D

P

I

A

E

F

R

Y

Y

A

A

E

H

V

F

I

L

active site: K53 (= K52), S78 (= S77), E204 (= E204), G208 (≠ W208), D210 (= D210), G232 (≠ A234), I303 (≠ V305), S304 (= S306)
binding magnesium ion: E204 (= E204), G208 (≠ W208), D210 (= D210)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F51), K53 (= K52), S77 (= S76), S78 (= S77), N80 (= N79), H81 (= H80), P147 (≠ S146), G179 (= G183), G180 (= G184), G181 (= G185), G182 (= G186), G232 (≠ A234), E277 (= E279), T279 (≠ G281), S304 (= S306)

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: 15:311/330 of query aligns to 27:328/339 of Q7XSN8

query
sites
Q7XSN8

A

A

A

Q

E

A

R

R

L

I

R

A

G

P

H

Y

V

V

T

H

E

K

T

T

P

P

L

V

L

L

P

S

L

S

-

T

-

S

-

I

-

D

A

A

W

I

Q

V

G

G

R

K

R

Q

L

L

W

F

I

F

K

K

A

C

E

E

C

C

L

F

Q

Q

Q

K

G

A

G

G

S

A

F

F

K

K

L

I

R

R

G

G

A

A

M

S

N

N

R

S

L

I

L

F

Q

A

L

L

D

D

A

D

Q

E

K

A

A

S

A

K

G

G

V

V

A

T

F

H

S

S

G

G

N

N

H

H

A

A

Q

A

G

A

V

V

A

A

L

L

A

A

R

K

Q

L

L

R

G

G

I

I

A

P

A

A

T

Y

I

I

V

V

M

I

P

P

H

R

D

N

A

A

P

P

A

A

V

C

K

K

R

V

D

D

A

N

T

V

L

K

A

R

A

Y

G

G

A

G

S

H

V

I

G

W

Y

S

D

D

R

V

L

S

R

I

E

E

S

S

R

R

E

E

S

S

I

V

G

A

A

K

R

R

L

V

A

Q

E

E

R

T

G

G

A

A

V

I

L

L

V

V

P

H

S

P

F

F

D

N

V

K

D

N

V

T

I

I

E

S

G

G

Q

Q

G

G

S

T

A

V

G

S

V

L

E

E

I

L

G

L

R

E

Q

E

M

V

A

P

A

E

L

I

A

-

D

-

G

-

P

-

E

D

M

T

V

I

L

I

V

V

C

P

C

I

G

S

G

G

L

L

S

I

A

S

G

G

I

V

A

A

L

L

A

A

L

A

-

K

-

A

-

I

-

N

P

P

D

S

A

I

E

R

I

I

V

L

T

A

V

A

E
|
E

P

P

E

K

G

G

W

A

D

D

D
|
D

M

S

A

A

Q

Q

S

S

L

K

A

A

S

A

G

G

A

K

I

I

V

I

E

T

V

L

G

-

K

-

D

P

A

S

P

T

P

N

T

T

R

I

C

A

D

D

A

G

L

L

Q

R

T

A

T

F

R

-

V

L

S

G

P

D

L

L

T

T

F

W

E

P

A

V

L

V

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

I

A

V

V

V

S

D

E

D

G

N

E

A

V

I

Q

V

A

D

A

A

M

M

A

K

F

M

A

C

A

Y

R

E

H

M

L

L

R

K

L

V

V

A

A

V

E

E

P

P

G

S

G

G

A

A

V

I

A

G

L

L

A

A

L

L

S

S

-

D

-

E

-

F

-

K

-

Q

G

S

R

S

A

A

G

W

P

H

L

E

P

S

A

S

R

K

T

I

A

G

I

I

L

I

V

V

S

S

G

G

N

N

V

V

D

D

E219 (= E204) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D210) 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)
38% identity, 90% coverage: 15:311/330 of query aligns to 11:312/329 of 5cvcA

query
sites
5cvcA

A

A

A

Q

E

A

R

R

L

I

R

A

G

P

H

Y

V

V

T

H

E

R

T

T

P

P

L

V

L

M

P

S

L

S

-

T

-

S

-

I

-

D

A

A

W

M

Q

V

G

G

R

K

L

L

W

F

I

F

K

K

A

C

E

E

C

C

L

F

Q

Q

Q

K

G

A

G

G

S

A

F
|
F

K
|
K

L

I

R

R

G

G

A

A

M

S

N

N

R

S

L

I

L

F

Q

A

L

L

D

D

A

E

Q

Q

K

V

A

S

A

K

G

G

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

A

G

A

V

V

A

A

L

L

A

A

R

K

Q

L

L

R

G

G

I

I

A

P

A

A

T

H

I

I

V

V

M

I

P

P

H

R

D

N

A

A

P

P

A

A

V

S

K

K

R

V

D

E

A

N

T

V

L

K

A

C

A

Y

G

G

A

G

S

H

V

I

G

W

Y

S

D

D

R

A

L

S

R

I

E

E

S

S

R

R

E

E

S

Y

I

V

G

S

A

K

R

R

L

V

A

Q

E

E

R

T

G

G

A

A

V

V

L

L

V

I

P

H

S

P

F

I

D

N

D

S

V

K

D

Y

V

T

I

I

E

S

G

G

Q

Q

G

G

S

T

A

V

G

S

V

L

E

E

I

L

G

L

R

E

Q

Q

M

V

A

P

A

E

L

I

A

-

D

-

G

-

P

-

E

D

M

T

V

I

L

I

V

V

C

P

C

I

G
x
S

G
|
G

L

L

S

I

A

S

G

G

I

V

A

A

L

L

A

A

L

A

-

K

-

A

-

I

-

N

P

P

D

S

A

I

E

R

I

I

V

L

T

A

V

A

E
|
E

P

P

E

K

G

G

W
x
A

D

D

D
|
D

M

S

A

A

Q

Q

S

S

L

K

A

A

S

A

G

G

A

K

I

I

V

I

E

T

V

L

G

-

K

-

D

P

A

S

P

T

P

N

T

T

R

I

C

A

D

D

A
x
G

L
|
L

Q

R

T

A

T

F

R

-

V

L

S

G

P

D

L

L

T

T

F

W

E

P

A

V

L

V

R

R

D

D

A

L

G

V

A

D

R

D

G

V

V

I

A

V

V

V

S

D

E

D

G

T

E

A

V

I

Q

V

A

D

A

A

M

M

A

K

F

M

A

C

A

Y

R

E

H

I

L

L

R

K

L

V

V

A

A

V

E
|
E

P

P

G

S

G

G

A

A

V

I

A

G

L

L

A

A

L

L

S

S

-

D

-

E

-

F

-

K

-

Q

G

S

R

S

A

A

G

W

P

H

L

E

P

S

A

S

R

K

T

I

A

G

I

I

L

I

V
|
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K52 (= K52), S77 (= S77), E203 (= E204), A207 (≠ W208), D209 (= D210), G231 (≠ A234), V306 (= V305), S307 (= S306)
binding magnesium ion: E203 (= E204), A207 (≠ W208), D209 (= D210)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), S178 (≠ G183), G179 (= G184), G180 (= G185), G181 (= G186), L232 (= L235), E275 (= E279), S307 (= S306), G308 (= G307)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 92% coverage: 10:311/330 of query aligns to 7:310/310 of 7nbgDDD

query
sites
7nbgDDD

A

A

G

D

V

V

V

E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T

H

E

L

T

T

P

P

L

V

L

L

P

T

L

S

A

S

-

I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L

F

Q

Q

Q

K

G

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

M

L

N

N

R

A

L

V

L

R

Q

S

L

L

D

-

A

V

Q

R

K

K

A

P

A

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

L

E

G

G

I

I

A

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

H

Q

D

T

A

A

P

P

A

D

V

C

K

K

R

K

D

L

A

A

T

I

L

Q

A

A

A
x
Y

G

G

A

A

S

S

V

I

V

V

G

Y

Y

C

D

E

R

P

L

S

R

D

E

E

S

S

R

R

E

E

S

N

I

V

G

A

A

K

R

R

L

V

A

T

E

E

R

T

G

E

A

G

V

I

L

M

V

V

P

H

S

P

F

N

D

Q

D

E

V

P

D

A

V

V

I

I

E

A

G

G

Q

Q

G

G

S

T

A

I

G

A

V

L

E

E

I

V

G

L

R

N

Q

Q

M

V

A

-

A

P

L

L

A

V

D

D

G

A

P

-

E

-

M

-

V

L

L

V

V

V

C

P

C

V

G
|
G

L
x
M

S

L

A

A

G

G

I

I

A

A

L

I

A

T

L

V

-

K

-

A

-

L

-

K

P

P

D

S

A

V

E

K

I

V

V

Y

T

A

V

A

E
|
E

P

P

E

S

G

N

W
x
A

D

D

D
|
D

M

C

A

Y

Q

Q

S

S

L

K

A

L

S

K

G

G

A

K

I

L

V

M

E

P

V

-

G

N

K

L

D

Y

A

P

P

P

P

E

T

T

R

I

C

A

D

D

A
x
G

L
x
V

Q

K

T

S

R

-

V

I

S

G

P

L

L
x
N

T

T

F

W

E

P

A

I

L

I

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

F

A

T

V

V

S

T

E

E

G

D

E

E

V

I

Q

K

A

C

A

A

M

T

A

Q

F

L

A

V

A

W

R

E

H

R

L

M

R

K

L

L

V

L

A

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

S

S

G

Q

R

H

-

F

-

Q

-

T

A

V

G

S

P

P

L

E

P

V

A

K

R

N

T

I

A

C

I

I

L

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S76 (= S77), E202 (= E204), A206 (≠ W208), D208 (= D210), G231 (≠ A234), L304 (≠ V305), S305 (= S306)
binding calcium ion: E202 (= E204), A206 (≠ W208), D208 (= D210)
binding magnesium ion: N239 (≠ L243)
binding ortho-xylene: S76 (= S77), Q81 (= Q82), I96 (= I97), Y113 (≠ A114)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N78 (= N79), G177 (= G183), G178 (= G184), G179 (= G185), G180 (= G186), M181 (≠ L187), G231 (≠ A234), V232 (≠ L235), E275 (= E279), T277 (≠ G281), S305 (= S306), G306 (= G307)

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)
35% identity, 92% coverage: 10:311/330 of query aligns to 8:311/322 of 3l6bA

query
sites
3l6bA

A

A

G

D

V

V

V

E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T

H

E

L

T

T

P

P

L

V

L

L

P

T

L

S

A

S

-

I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L

F

Q

Q

Q

K

G

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

M

L

N

N

R

A

L

V

L

R

Q

S

L

L

D

-

A

V

Q

R

K

K

A

P

A

K

G

A

V

V

A

T

F

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

L

E

G

G

I

I

A

P

A

A

T

Y

I

I

V

V

M

V

P

P

H

Q

D

T

A

A

P

P

A

D

V

C

K

K

R

K

D

L

A

A

T

I

L

Q

A

A

A

Y

G

G

A

A

S

S

V

I

V

V

G

Y

Y

C

D

E

R

P

L

S

R

D

E

E

S

S

R
|
R

E

E

S

N

I

V

G

A

A

K

R

R

L

V

A

T

E

E

R

T

G

E

A

G

V

I

L

M

V

V

P

H

S

P

F

N

D

Q

D

E

V

P

D

A

V

V

I

I

E

A

G

G

Q

Q

G

G

S

T

A

I

G

A

V

L

E

E

I

V

G

L

R

N

Q

Q

M

V

A

-

A

P

L

L

A

V

D

D

G

A

P

-

E

-

M

-

V

L

L

V

V

V

C

P

C

V

G
|
G

L
x
M

S

L

A

A

G

G

I

I

A

A

L

I

A

T

L

V

-

K

-

A

-

L

-

K

P

P

D

S

A

V

E

K

I

V

V

Y

T

A

V

A

E
|
E

P

P

E

S

G

N

W
x
A

D

D

D
|
D

M

C

A

Y

Q

Q

S

S

L

K

A

L

S

K

G

G

A

K

I

L

V

M

E

P

V

-

G

N

K

L

D

Y

A

P

P

P

P

E

T

T

R

I

C

A

D

D

A
x
G

L
x
V

Q

K

T

S

R

-

V

I

S

G

P

L

L

N

T

T

F

W

E

P

A

I

L

I

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

F

A

T

V

V

S

T

E

E

G

D

E

E

V

I

Q

K

A

C

A

A

M

T

A

Q

F

L

A

V

A

W

R

E

H

R

L

M

R

K

L

L

V

L

A

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

S

S

G

Q

R

H

-

F

-

Q

-

T

A

V

G

S

P

P

L

E

P

V

A

K

R

N

T

I

A

C

I

I

L

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K54 (= K52), S77 (= S77), E203 (= E204), A207 (≠ W208), D209 (= D210), G232 (≠ A234), T278 (≠ G281), L305 (≠ V305), S306 (= S306)
binding malonate ion: K54 (= K52), S76 (= S76), S77 (= S77), N79 (= N79), H80 (= H80), R128 (= R128), G232 (≠ A234)
binding manganese (ii) ion: E203 (= E204), A207 (≠ W208), D209 (= D210)
binding pyridoxal-5'-phosphate: F53 (= F51), K54 (= K52), N79 (= N79), G178 (= G183), G179 (= G184), G180 (= G185), G181 (= G186), M182 (≠ L187), V233 (≠ L235), E276 (= E279), T278 (≠ G281), S306 (= S306), G307 (= G307)

6zspAAA serine racemase bound to atp and malonate. (see paper)
35% identity, 92% coverage: 10:311/330 of query aligns to 7:308/320 of 6zspAAA

query
sites
6zspAAA

A

A

G

D

V

V

V

E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T

H

E

L

T

T

P

P

L

V

L

L

P

T

L
x
S

A
x
S

-
x
I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L

F

Q

Q

Q
x
K

G
x
T

G

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

M

L

N

N

R

A

L

V

L

R

Q

S

L

L

D

-

A

-

Q

-

K

K

A

P

A

K

G

A

V

V

A

T

F

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

L

E

G

G

I

I

A

P

A

A

T

Y

I

I

V

V

M

V

P

P

H

Q

D

T

A

A

P

P

A

D

V

C

K

K

R

K

D

L

A

A

T

I

L

Q

A

A

A
x
Y

G

G

A

A

S

S

V

I

V

V

G

Y

Y

C

D

E

R

P

L

S

R

D

E

E

S

S

R
|
R

E

E

S

N

I

V

G

A

A

K

R

R

L

V

A

T

E

E

R

T

G

E

A

G

V

I

L

M

V

V

P

H

S

P

F

N

D

Q

D

E

V

P

D

A

V

V

I

I

E

A

G

G

Q

Q

G

G

S

T

A

I

G

A

V

L

E

E

I

V

G

L

R

N

Q

Q

M

V

A

-

A

P

L

L

A

V

D

D

G

A

P

-

E

-

M

-

V

L

L

V

V

V

C

P

C

V

G

G

L

M

S

L

A

A

G

G

I

I

A

A

L

I

A

T

L

V

-

K

-

A

-

L

-

K

P

P

D

S

A

V

E

K

I

V

V

Y

T

A

V

A

E
|
E

P

P

E

S

G

N

W
x
A

D

D

D
|
D

M

C

A

Y

Q

Q

S

S

L

K

A

L

S

K

G

G

A

K

I

L

V

M

E

P

V

-

G

N

K

L

D

Y

A

P

P

P

P

E

T

T

R

I

C

A

D

D

A
x
G

L

V

Q

K

T
x
S

T

S

R

-

V

I

S

G

P

L

L

N

T

T

F

W

E

P

A

I

L

I

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

F

A

T

V

V

S

T

E

E

G

D

E

E

V

I

Q

K

A

C

A

A

M

T

A

Q

F

L

A

V

A

W

R
x
E

H
x
R

L

M

R
x
K

L

L

V

L

A

I

E

E

P

P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

S

S

G

Q

R

H

-

F

-

Q

-

T

A

V

G

S

P

P

L

E

P

V

A

K

R

N

T

I

A

C

I

I

L

V

V
x
L

S
|
S

G

G

N
|
N

V

V

D

D

active site: K53 (= K52), S74 (= S77), E200 (= E204), A204 (≠ W208), D206 (= D210), G229 (≠ A234), L302 (≠ V305), S303 (= S306)
binding adenosine-5'-triphosphate: S28 (≠ L31), S29 (≠ A32), I30 (vs. gap), K48 (≠ Q47), T49 (≠ G48), Q79 (= Q82), Y111 (≠ A114), E266 (≠ R272), R267 (≠ H273), K269 (≠ R275), N306 (= N309)
binding magnesium ion: E200 (= E204), A204 (≠ W208), D206 (= D210)
binding malonate ion: K53 (= K52), S73 (= S76), S74 (= S77), N76 (= N79), H77 (= H80), R125 (= R128), G229 (≠ A234), S232 (≠ T237)

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, 92% coverage: 10:311/330 of query aligns to 10:318/340 of Q9GZT4

query
sites
Q9GZT4

A

A

G

D

V

V

V
x
E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T

H

E

L

T

T

P

P

L

V

L

L

P

T

L
x
S

A
x
S

-
x
I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L

F

Q

Q

Q
x
K

G
x
T

G

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

M

L

N

N

R

A

L

V

L

R

Q

S

L

L

-

V

D
x
P

D

D

A

A

-

L

-

E

Q

R

K

K

A

P

A

K

G

A

V

V

A
x
T

F

H

S

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

L

E

G

G

I

I

A

P

A

A

T

Y

I

I

V

V

M

V

P

P

H

Q

D

T

A

A

P

P

A

D

V

C

K

K

R

K

D

L

A

A

T

I

L

Q

A

A

A
x
Y

G

G

A

A

S

S

V

I

V

V

G

Y

Y

C

D

E

R

P

L

S

R

D

E

E

S

S

R

R

E

E

S

N

I

V

G

A

A

K

R

R

L

V

A

T

E

E

R

T

G

E

A

G

V

I

L

M

V

V

P

H

S

P

F

N

D

Q

D

E

V

P

D

A

V

V

I

I

E

A

G

G

Q

Q

G

G

S

T

A

I

G

A

V

L

E

E

I

V

G

L

R

N

Q

Q

M

V

A

-

A

P

L

L

A

V

D
|
D

G

A

P

-

E

-

M

-

V

L

L

V

V

V

C

P

C

V

G
|
G

L
x
M

S

L

A

A

G

G

I

I

A

A

L

I

A

T

L

V

-

K

-

A

-

L

-

K

P

P

D

S

A

V

E

K

I

V

V

Y

T

A

V

A

E
|
E

P

P

E

S

G

N

W
x
A

D

D

D
|
D

M

C

A

Y

Q

Q

S

S

L

K

A

L

S

K

G

G

A

K

I

L

V

M

E

P

V

-

G

N

K

L

D

Y

A

P

P

P

P

E

T

T

R

I

C

A

D

D

A

G

L

V

Q

K

T

S

R

-

V

I

S

G

P

L

L
x
N

T

T

F

W

E

P

A

I

L

I

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

F

A

T

V

V

S

T

E

E

G

D

E

E

V

I

Q

K

A

C

A

A

M

T

A

Q

F

L

A

V

A

W

R

E

H

R

L

M

R
x
K

L

L

V

L

A

I

E

E

P

P

G

T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

S

S

G

Q

R

H

-

F

-

Q

-

T

A

V

G

S

P

P

L

E

P

V

A

K

R

N

T

I

A

C

I

I

L

V

V

L

S
|
S

G

G

N
|
N

V

V

D

D

E13 (≠ V13) binding Mg(2+)
S31 (≠ L31) binding ATP
S32 (≠ A32) binding ATP
I33 (vs. gap) binding ATP
K51 (≠ Q47) binding ATP
T52 (≠ G48) binding ATP
K56 (= K52) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ D64) binding Ca(2+)
T81 (≠ A74) binding Ca(2+)
N86 (= N79) binding pyridoxal 5'-phosphate
Q89 (= Q82) binding ATP
Y121 (≠ A114) binding ATP
D178 (= D172) binding Mg(2+)
G185 (= G183) binding pyridoxal 5'-phosphate
G186 (= G184) binding pyridoxal 5'-phosphate
G187 (= G185) binding pyridoxal 5'-phosphate
G188 (= G186) binding pyridoxal 5'-phosphate
M189 (≠ L187) binding pyridoxal 5'-phosphate
E210 (= E204) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ W208) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (= D210) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L243) binding Ca(2+); binding Mg(2+)
K279 (≠ R275) binding ATP
S313 (= S306) binding pyridoxal 5'-phosphate
N316 (= N309) binding ATP

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
35% identity, 92% coverage: 10:311/330 of query aligns to 7:315/323 of 7nbfAAA

query
sites
7nbfAAA

A

A

G

D

V

V

V

E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T
x
H

E
x
L

T
|
T

P
|
P

L

V

L
|
L

P
x
T

L

S

A

S

-

I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L
x
F

Q

Q

Q

K

G

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

M

L

N

N

R

A

L

V

L

R

Q

S

L

L

-

V

D

P

D

D

A

A

-

L

-

E

Q

R

K

K

A

P

A

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

Q

L

L

E

G

G

I

I

A

P

A

A

T

Y

I

I

V

V

M

V

P

P

H

Q

D

T

A

A

P

P

A

D

V

C

K

K

R

K

D

L

A

A

T

I

L

Q

A

A

A

Y

G

G

A

A

S

S

V

I

V

V

G

Y

Y

C

D

E

R

P

L

S

R

D

E

E

S

S

R

R

E

E

S

N

I

V

G

A

A

K

R

R

L

V

A

T

E

E

R

T

G

E

A

G

V

I

L

M

V

V

P

H

S

P

F

N

D

Q

D

E

V

P

D

A

V

V

I

I

E

A

G

G

Q

Q

G

G

S

T

A

I

G

A

V

L

E

E

I

V

G

L

R

N

Q

Q

M

V

A

-

A

P

L

L

A

V

D

D

G

A

P

-

E

-

M

-

V

L

L

V

V

V

C

P

C

V

G
|
G

L
x
M

S

L

A

A

G

G

I

I

A

A

L

I

A

T

L

V

-

K

-

A

-

L

-

K

P

P

D

S

A

V

E

K

I

V

V

Y

T

A

V

A

E
|
E

P

P

E

S

G

N

W
x
A

D

D

D
|
D

M

C

A

Y

Q

Q

S

S

L

K

A

L

S

K

G

G

A

K

I

L

V

M

E

P

V

-

G

N

K

L

D

Y

A

P

P

P

P

E

T

T

R

I

C

A

D

D

A
x
G

L
x
V

Q

K

T

S

R

-

V

I

S

G

P

L

L
x
N

T

T

F

W

E

P

A

I

L

I

R

R

D

D

A

L

G

V

A

D

R

D

G

I

V

F

A

T

V

V

S

T

E

E

G

D

E

E

V

I

Q

K

A

C

A

A

M

T

A

Q

F

L

A

V

A

W

R

E

H

R

L

M

R

K

L

L

V

L

A

I

E

E

P

P

G
x
T

G

A

A

G

V

V

A

G

L

V

A

A

A

V

L

L

S

S

G

Q

R

H

-

F

-

Q

-

T

A

V

G

S

P

P

L

E

P

V

A

K

R

N

T

I

A

C

I

I

L

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E204), A211 (≠ W208), D213 (= D210), G236 (≠ A234), L309 (≠ V305), S310 (= S306)
binding calcium ion: E207 (= E204), A211 (≠ W208), D213 (= D210)
binding magnesium ion: N244 (≠ L243)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G183), G183 (= G184), G184 (= G185), G185 (= G186), M186 (≠ L187), G236 (≠ A234), V237 (≠ L235), T282 (≠ G281), S310 (= S306), G311 (= G307)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ T24), L22 (≠ E25), T23 (= T26), P24 (= P27), L26 (= L29), T27 (≠ P30), F46 (≠ L45)

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, 92% coverage: 10:311/330 of query aligns to 7:315/323 of 7nbdAAA

query
sites
7nbdAAA

A

A

G

D

V

V

V

E

A

K

A

A

A

H

E

I

R

N

L

I

R

R

G

D

H

S

V

I

T

H

E

L

T

T

P

P

L

V

L

L

P

T

L

S

A

S

-

I

-

L

-

N

-

Q

W

L

Q

T

G

G

R

R

R

N

L

L

W

F

I

F

K

K

A

C

E

E

C

L

L

F

Q

Q

Q

K

G

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G