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, 97% coverage: 5:320/326 of query aligns to 7:321/323 of O59791

query
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O59791

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K57 (= K55) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S80) 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 (= N82) binding pyridoxal 5'-phosphate
G183 (≠ S182) binding pyridoxal 5'-phosphate
G184 (= G183) binding pyridoxal 5'-phosphate
G185 (= G184) binding pyridoxal 5'-phosphate
G186 (= G185) binding pyridoxal 5'-phosphate
L187 (= L186) binding pyridoxal 5'-phosphate
E208 (= E207) binding Mg(2+)
G212 (≠ F211) binding Mg(2+)
D214 (= D213) binding Mg(2+)
S308 (= S307) binding pyridoxal 5'-phosphate

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
38% identity, 97% coverage: 5:320/326 of query aligns to 3:317/319 of 2zr8A

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active site: K53 (= K55), S78 (= S80), E204 (= E207), G208 (≠ F211), D210 (= D213), G232 (≠ A236), I303 (≠ L306), S304 (= S307)
binding magnesium ion: E204 (= E207), G208 (≠ F211), D210 (= D213)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F54), K53 (= K55), S77 (= S79), S78 (= S80), N80 (= N82), H81 (= H83), P147 (= P149), G179 (≠ S182), G180 (= G183), G181 (= G184), G182 (= G185), G232 (≠ A236), E277 (= E280), T279 (≠ G282), S304 (= S307)
binding serine: S78 (= S80), R129 (= R131), D231 (= D235), G232 (≠ A236), A233 (≠ L237), Q234 (≠ M238), T235 (≠ S239)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
38% identity, 97% coverage: 5:320/326 of query aligns to 3:317/319 of 2zpuA

query
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active site: K53 (= K55), S78 (= S80), E204 (= E207), G208 (≠ F211), D210 (= D213), G232 (≠ A236), I303 (≠ L306), S304 (= S307)
binding magnesium ion: E204 (= E207), G208 (≠ F211), D210 (= D213)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F54), K53 (= K55), S77 (= S79), S78 (= S80), N80 (= N82), H81 (= H83), P147 (= P149), G179 (≠ S182), G180 (= G183), G181 (= G184), G182 (= G185), G232 (≠ A236), E277 (= E280), T279 (≠ G282), S304 (= S307)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
38% identity, 97% coverage: 5:320/326 of query aligns to 2:316/318 of 1wtcA

query
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1wtcA

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Q

M

H

P

L

G

G

V

N

L

Y

T

T

W

F

P

S

-

I

I

I

N

K

R

E

R

K

L

V

A

D

G

D

A

I

I

L

T

T

V

V

S

S

D

D

G

E

E

E

V

L

A

I

E

D

A

C

M

L

R

K

F

F

A

Y

F

A

R

A

H

R

L

M

K

K

I

I

V

V

L

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

S

S

L

F

A

A

L

A

L

R

A

A

G

M

K

K

I

E

G

K

T

L

K

K

G

N

R

K

T

R

T

I

A

G

M

I

V

I

L
x
I

S
|
S

G

G

N

N

V

V

D

D

P

I

T

E

L

R

Y

Y

A

A

E

H

I

F

I

L

active site: K52 (= K55), S77 (= S80), E203 (= E207), G207 (≠ F211), D209 (= D213), G231 (≠ A236), I302 (≠ L306), S303 (= S307)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ V23), K47 (≠ R50), M48 (≠ A51), A109 (≠ E112), A110 (≠ G113), Y114 (≠ F117)
binding magnesium ion: E203 (= E207), G207 (≠ F211), D209 (= D213)
binding pyridoxal-5'-phosphate: F51 (= F54), K52 (= K55), N79 (= N82), G178 (≠ S182), G179 (= G183), G180 (= G184), G181 (= G185), G231 (≠ A236), E276 (= E280), T278 (≠ G282), S303 (= S307)

1v71A Crystal structure of s.Pombe serine racemase
38% identity, 97% coverage: 5:320/326 of query aligns to 2:316/318 of 1v71A

query
sites
1v71A

V

L

P

P

S

T

Y

Y

E

D

G

D

V

V

L

A

D

S

A

A

A

S

R

E

Q

R

I

I

D

K

G

K

V

F

A

A

V

N

R

K

T

T

P

P

L

V

L

L

E

T

S

S

P

S

A

T

L

V

N

N

A

K

V

E

V

F

G

V

G

A

R

E

V

V

M

F

K

K

A

C

E

E

S

N

L

F

Q

Q

R

K

A

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

Y

L

N

N

R

A

I

L

S

S

R

Q

L

L

T

N

D

E

E

A

E

Q

K

R

A

K

R

A

G

G

V

V

V

L

A

T

F

F

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

A

L

A

S

A

A

A

K

M

I

V

L

G

G

T

I

P

P

A

A

I

K

I

I

V

I

M

M

P

P

S

L

D

D

S

A

P

P

R

E

V

A

K

K

V

V

E

A

G

A

V

T

I

K

G

G

F

Y

G

G

E

Q

V

V

R

I

F

M

Y

Y

D

D

R

R

W

Y

T

K

E

D

S

D

R

R

E

E

A

K

I

M

G

A

A

K

A

E

I

I

A

S

A

E

E

R

R

E

G

G

S

L

I

T

L

I

V

I

P

P

F

Y

D

D

D

H

P

P

F

H

I

V

V

L

E

A

G

G

Q

Q

G

G

T

T

T

A

A

A

L

K

E

E

M

L

L

F

D

E

Q

E

A

V

D

-

A

G

P

P

F

L

D

D

Q

A

L

L

L

F

C

V

G

C

A

L

S
x
G

G
|
G

L

L

M

L

A

S

G

G

I

S

N

A

L

L

V

A

M

A

A

R

E

H

R

F

S

A

P

P

A

N

T

C

K

E

V

V

F

Y

V

G

V

V

E
|
E

P

P

E

E

A

A

F
x
G

D

N

D
|
D

T

G

A

Q

R

Q

S

S

L

F

A

R

A

K

G

G

E

S

R

I

V

V

G

-

H

H

P

I

Q

D

G

T

A

P

P

K

S

T

I

I

C

A

D

D

A
x
G

L

A

M

Q

S

T

P

Q

M

H

P

L

G

G

V

N

L

Y

T

T

W

F

P

S

-

I

I

I

N

K

R

E

R

K

L

V

A

D

G

D

A

I

I

L

T

T

V

V

S

S

D

D

G

E

E

E

V

L

A

I

E

D

A

C

M

L

R

K

F

F

A

Y

F

A

R

A

H

R

L

M

K

K

I

I

V

V

L

V

E
|
E

P

P

G
x
T

G

G

A

C

V

L

S

S

L

F

A

A

L

A

L

R

A

A

G

M

K

K

I

E

G

K

T

L

K

K

G

N

R

K

T

R

T

I

A

G

M

I

V

I

L
x
I

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

I

T

E

L

R

Y

Y

A

A

E

H

I

F

I

L

active site: K52 (= K55), S77 (= S80), E203 (= E207), G207 (≠ F211), D209 (= D213), G231 (≠ A236), I302 (≠ L306), S303 (= S307)
binding magnesium ion: E203 (= E207), G207 (≠ F211), D209 (= D213)
binding pyridoxal-5'-phosphate: F51 (= F54), K52 (= K55), N79 (= N82), G178 (≠ S182), G179 (= G183), G180 (= G184), G181 (= G185), G231 (≠ A236), E276 (= E280), T278 (≠ G282), S303 (= S307), G304 (= G308)

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, 92% coverage: 24:323/326 of query aligns to 37:339/339 of Q7XSN8

query
sites
Q7XSN8

R

K

T

T

P

P

L

V

L

L

E

S

S

S

P

T

A

S

L

I

N

D

A

A

V

I

V

V

G

G

G

K

R

Q

V

L

M

F

K

K

A

C

E

E

S

C

L

F

Q

Q

R

K

A

A

G

G

A

A

F

F

K

K

F

I

R

R

G

G

A

A

Y

S

N

N

R

S

I

I

S

F

R

A

L

L

T

D

D

D

E

D

E

E

K

A

A

S

R

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

A

L

A

A

A

K

M

L

V

R

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

I

P

P

S

R

D

N

S

A

P

P

R

A

V

C

K

K

V

V

E

D

G

N

V

V

I

K

G

R

F

Y

G

G

E

H

V

I

R

I

F

W

Y

S

D

D

R

V

W

S

T

I

E

E

S

S

R

R

E

E

A

S

I

V

G

A

A

K

A

R

I

V

A

Q

A

E

E

E

R

T

G

G

S

A

I

I

L

L

V

V

P

H

P

P

F

F

D

N

P

K

F

N

I

T

V

I

E

S

G

G

Q

Q

G

G

T

T

T

V

A

S

L

L

E

E

M

L

L

L

D

E

Q

E

A

V

D

-

A

P

P

E

F

I

D

D

Q

T

L

I

C

V

G

P

A

I

S

S

G

G

L

L

M

I

A

S

G

G

I

V

N

A

L

L

V

A

M

A

A

K

E

A

R

I

S

N

P

P

A

S

T

I

K

R

V

I

F

L

V

A

E
|
E

P

P

E

K

A

G

F

A

D

D

D
|
D

T

S

A

A

R

Q

S

S

L

K

A

A

G

G

E

K

R

I

V

I

G

T

H

L

P

P

Q

S

G

-

A

T

P

N

S

T

I

I

C

A

D

D

A

G

L

L

M

R

S

A

P

F

M

L

P

-

G

G

V

D

L

L

T

T

W

W

P

P

I

V

N

V

R

R

R

D

L

L

A

V

-

D

G

D

A

I

I

I

T

V

V

V

S

D

D

D

G

N

E

A

V

I

A

V

E

D

A

A

M

M

R

K

F

M

A

C

F

Y

R

E

H

M

L

L

K

K

I

V

V

A

L

V

E

E

P

P

G

S

G

G

A

A

V

I

S

G

L

L

A

A

L

A

L

L

A

S

G

D

K

E

I

F

G

K

T

Q

-

S

-

A

-

W

-

H

K

E

G

S

R

S

T

K

T

I

A

G

M

I

V

I

L

V

S

S

G

G

N

N

V

V

D

D

P

L

T

G

L

V

Y

L

A

W

E

E

I

S

I

L

E

Y

G

K

R

R

E219 (= E207) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D213) 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, 93% coverage: 9:312/326 of query aligns to 6:312/329 of 5cvcA

query
sites
5cvcA

E

D

G

S

V

I

L

R

D

E

A

A

A

Q

R

A

Q

R

I

I

D

A

G

P

V

Y

A

V

V

H

R

R

T

T

P

P

L

V

L

M

E

S

S

S

P

T

A

S

L

I

N

D

A

A

V

M

V

V

G

G

G

K

R

K

V

L

M

F

K

K

A

C

E

E

S

C

L

F

Q

Q

R

K

A

A

G

G

A

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

S

N

N

R

S

I

I

S

F

R

A

L

L

T

D

D

D

E

E

E

Q

K

V

A

S

R

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

A

L

A

A

A

K

M

L

V

R

G

G

T

I

P

P

A

A

I

H

I

I

V

V

M

I

P

P

S

R

D

N

S

A

P

P

R

A

V

S

K

K

V

V

E

E

G

N

V

V

I

K

G

C

F

Y

G

G

E

H

V

I

R

I

F

W

Y

S

D

D

R

A

W

S

T

I

E

E

S

S

R

R

E

E

A

Y

I

V

G

S

A

K

A

R

I

V

A

Q

A

E

E

E

R

T

G

G

S

A

I

V

L

L

V

I

P

H

P

P

F

I

D

N

D

S

P

K

F

Y

I

T

V

I

E

S

G

G

Q

Q

G

G

T

T

T

V

A

S

L

L

E

E

M

L

L

L

D

E

Q

Q

A

V

D

-

A

P

P

E

F

I

D

D

Q

T

L

I

C

V

G

P

A

I

S
|
S

G
|
G

L

L

M

I

A

S

G

G

I

V

N

A

L

L

V

A

M

A

A

K

E

A

R

I

S

N

P

P

A

S

T

I

K

R

V

I

F

L

V

A

E
|
E

P

P

E

K

A

G

F
x
A

D

D

D
|
D

T

S

A

A

R

Q

S

S

L

K

A

A

G

G

E

K

R

I

V

I

G

T

H

L

P

P

Q

-

G

S

A

T

P

N

S

T

I

I

C

A

D

D

A
x
G

L
|
L

M

R

S

A

P

F

M

L

P

-

G

G

V

D

L

L

T

T

W

W

P

P

I

V

N

V

R

R

R

D

L

L

A

V

G

D

A

D

I

V

T

I

V

V

S

V

D

D

G

D

E

T

-

A

V

I

A

V

E

D

A

A

M

M

R

K

F

M

A

C

F

Y

R

E

H

I

L

L

K

K

I

V

V

A

L

V

E
|
E

P

P

G

S

G

G

A

A

V

I

S

G

L

L

A

A

L

A

L

L

A

S

G

D

K

E

I

F

G

K

T

Q

-

S

-

A

-

W

-

H

K

E

G

S

R

S

T

K

T

I

A

G

M

I

V

I

L
x
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K52 (= K55), S77 (= S80), E203 (= E207), A207 (≠ F211), D209 (= D213), G231 (≠ A236), V306 (≠ L306), S307 (= S307)
binding magnesium ion: E203 (= E207), A207 (≠ F211), D209 (= D213)
binding pyridoxal-5'-phosphate: F51 (= F54), K52 (= K55), N79 (= N82), S178 (= S182), G179 (= G183), G180 (= G184), G181 (= G185), L232 (= L237), E275 (= E280), S307 (= S307), G308 (= G308)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
36% identity, 89% coverage: 25:314/326 of query aligns to 23:317/322 of 7nbgAAA

query
sites
7nbgAAA

T

T

P

P

L

V

L

L

E

T

S

S

P

S

A

I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I
|
I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K
|
K

V

K

E

L

G

A

V
x
I

I

Q

G

A

F
x
Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

A

K

A

R

I

V

A

T

A

E

E

E

R

T

G

E

S

G

I

I

L

M

V

V

P

H

P

P

F

N

D

Q

D

E

P

P

F

A

I

V

V

I

E

A

G

G

Q

Q

G

G

T

T

T

I

A

A

L

L

E

E

M

V

L

L

D

N

Q

Q

A

V

D

P

A

L

P

-

F

V

D

D

Q

A

L

L

L

V

C

V

G

P

A

V

S
x
G

G
|
G

L
x
M

M

L

A

A

G

G

I

I

N

A

L

I

V

T

M

V

A

K

E

A

R

L

S

K

P

P

A

S

T

V

K

K

V

V

F

Y

V

A

E
|
E

P

P

E

S

A

N

F
x
A

D

D

D
|
D

T

C

A

Y

R

Q

S

S

L

K

A

L

A

K

G

G

E

K

R

L

V

M

G

P

H

N

P

L

Q

Y

G

P

A

P

P

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

M

K

S

S

P

S

M

I

P

-

G

G

V

L

L

N

T

T

W

W

P

P

I

I

N

I

R

R

R

D

L

L

A

V

G

D

A

D

I

I

-

F

T

T

V

V

S

T

D

E

G

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

F

L

A

V

F

W

R

E

H

R

L

M

K

K

I

L

V

L

L

I

E

E

P

P

G
x
T

G

A

A

G

V

V

S

G

L

V

A

A

L

V

L

L

A

S

G

Q

K

H

I

F

G

Q

T

T

-

V

-

S

-

P

K

E

G

V

R

K

T

N

T

I

A

C

M

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

L

T

T

active site: K53 (= K55), S81 (= S80), E207 (= E207), A211 (≠ F211), D213 (= D213), G236 (≠ A236), L309 (= L306), S310 (= S307)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (= D213)
binding pyridoxal-5'-phosphate: F52 (= F54), K53 (= K55), N83 (= N82), G182 (≠ S182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G282), S310 (= S307), G311 (= G308)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (= S80), G85 (≠ A84), Q86 (= Q85), I101 (= I100), K111 (= K110), I115 (≠ V114), Y118 (≠ F117)

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)
36% identity, 89% coverage: 25:314/326 of query aligns to 26:320/340 of Q9GZT4

query
sites
Q9GZT4

T

T

P

P

L

V

L

L

E

T

S
|
S

P
x
S

A
x
I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L

F

Q

Q

R
x
K

A
x
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D
x
P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

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

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K

K

V

K

E

L

G

A

V

I

I

Q

G

A

F
x
Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

A

K

A

R

I

V

A

T

A

E

E

E

R

T

G

E

S

G

I

I

L

M

V

V

P

H

P

P

F

N

D

Q

D

E

P

P

F

A

I

V

V

I

E

A

G

G

Q

Q

G

G

T

T

T

I

A

A

L

L

E

E

M

V

L

L

D

N

Q

Q

A

V

D

P

A

L

P

-

F

V

D
|
D

Q

A

L

L

L

V

C

V

G

P

A

V

S
x
G

G
|
G

L
x
M

M

L

A

A

G

G

I

I

N

A

L

I

V

T

M

V

A

K

E

A

R

L

S

K

P

P

A

S

T

V

K

K

V

V

F

Y

V

A

E
|
E

P

P

E

S

A

N

F
x
A

D

D

D
|
D

T

C

A

Y

R

Q

S

S

L

K

A

L

A

K

G

G

E

K

R

L

V

M

G

P

H

N

P

L

Q

Y

G

P

A

P

P

E

S

T

I

I

C

A

D

D

A

G

L

V

M

K

S

S

P

S

M

I

P

-

G

G

V

L

L
x
N

T

T

W

W

P

P

I

I

N

I

R

R

R

D

L

L

A

V

G

D

A

D

I

I

-

F

T

T

V

V

S

T

D

E

G

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

F

L

A

V

F

W

R

E

H

R

L

M

K
|
K

I

L

V

L

L

I

E

E

P

P

G

T

G

A

A

G

V

V

S

G

L

V

A

A

L

V

L

L

A

S

G

Q

K

H

I

F

G

Q

T

T

-

V

-

S

-

P

K

E

G

V

R

K

T

N

T

I

A

C

M

I

V

V

L

L

S
|
S

G

G

N
|
N

V

V

D

D

P

L

T

T

S31 (= S30) binding ATP
S32 (≠ P31) binding ATP
I33 (≠ A32) binding ATP
K51 (≠ R50) binding ATP
T52 (≠ A51) binding ATP
K56 (= K55) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ D68) binding Ca(2+)
T81 (≠ A77) binding Ca(2+)
N86 (= N82) binding pyridoxal 5'-phosphate
Q89 (= Q85) binding ATP
Y121 (≠ F117) binding ATP
D178 (= D175) binding Mg(2+)
G185 (≠ S182) binding pyridoxal 5'-phosphate
G186 (= G183) binding pyridoxal 5'-phosphate
G187 (= G184) binding pyridoxal 5'-phosphate
G188 (= G185) binding pyridoxal 5'-phosphate
M189 (≠ L186) binding pyridoxal 5'-phosphate
E210 (= E207) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ F211) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (= D213) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L245) binding Ca(2+); binding Mg(2+)
K279 (= K276) binding ATP
S313 (= S307) binding pyridoxal 5'-phosphate
N316 (= N310) binding ATP

Sites not aligning to the query:

13 binding Mg(2+)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
36% identity, 89% coverage: 25:314/326 of query aligns to 23:317/323 of 7nbfAAA

query
sites
7nbfAAA

T
|
T

P
|
P

L

V

L
|
L

E
x
T

S

S

P

S

A

I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L
x
F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

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

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K

K

V

K

E

L

G

A

V

I

I

Q

G

A

F

Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

A

K

A

R

I

V

A

T

A

E

E

E

R

T

G

E

S

G

I

I

L

M

V

V

P

H

P

P

F

N

D

Q

D

E

P

P

F

A

I

V

V

I

E

A

G

G

Q

Q

G

G

T

T

T

I

A

A

L

L

E

E

M

V

L

L

D

N

Q

Q

A

V

D

P

A

L

P

-

F

V

D

D

Q

A

L

L

L

V

C

V

G

P

A

V

S
x
G

G
|
G

L
x
M

M

L

A

A

G

G

I

I

N

A

L

I

V

T

M

V

A

K

E

A

R

L

S

K

P

P

A

S

T

V

K

K

V

V

F

Y

V

A

E
|
E

P

P

E

S

A

N

F
x
A

D

D

D
|
D

T

C

A

Y

R

Q

S

S

L

K

A

L

A

K

G

G

E

K

R

L

V

M

G

P

H

N

P

L

Q

Y

G

P

A

P

P

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

M

K

S

S

P

S

M

I

P

-

G

G

V

L

L
x
N

T

T

W

W

P

P

I

I

N

I

R

R

R

D

L

L

A

V

G

D

A

D

I

I

-

F

T

T

V

V

S

T

D

E

G

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

F

L

A

V

F

W

R

E

H

R

L

M

K

K

I

L

V

L

L

I

E

E

P

P

G
x
T

G

A

A

G

V

V

S

G

L

V

A

A

L

V

L

L

A

S

G

Q

K

H

I

F

G

Q

T

T

-

V

-

S

-

P

K

E

G

V

R

K

T

N

T

I

A

C

M

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

L

T

T

active site: K53 (= K55), S81 (= S80), E207 (= E207), A211 (≠ F211), D213 (= D213), G236 (≠ A236), L309 (= L306), S310 (= S307)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (= D213)
binding magnesium ion: N244 (≠ L245)
binding pyridoxal-5'-phosphate: F52 (= F54), K53 (= K55), N83 (= N82), G182 (≠ S182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G282), S310 (= S307), G311 (= G308)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: T23 (= T25), P24 (= P26), L26 (= L28), T27 (≠ E29), F46 (≠ L48)

Sites not aligning to the query:

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
36% identity, 89% coverage: 25:314/326 of query aligns to 23:317/323 of 7nbdAAA

query
sites
7nbdAAA

T

T

P

P

L

V

L

L

E

T

S

S

P

S

A

I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

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

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K

K

V

K

E

L

G

A

V

I

I

Q

G

A

F

Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

A

K

A

R

I

V

A

T

A

E

E

E

R

T

G

E

S

G

I

I

L

M

V

V

P

H

P

P

F

N

D

Q

D

E

P

P

F

A

I

V

V

I

E

A

G

G

Q

Q

G

G

T

T

T

I

A

A

L

L

E

E

M

V

L

L

D

N

Q

Q

A

V

D

P

A

L

P

-

F

V

D

D

Q

A

L

L

L

V

C

V

G

P

A

V

S
x
G

G
|
G

L
x
M

M

L

A

A

G

G

I

I

N

A

L

I

V

T

M

V

A

K

E

A

R

L

S

K

P

P

A

S

T

V

K

K

V

V

F

Y

V

A

E
|
E

P

P

E

S

A

N

F
x
A

D

D

D
|
D

T

C

A

Y

R

Q

S

S

L

K

A

L

A

K

G

G

E

K

R

L

V

M

G

P

H

N

P

L

Q

Y

G

P

A

P

P

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

M

K

S

S

P

S

M

I

P

-

G

G

V

L

L
x
N

T

T

W

W

P

P

I

I

N

I

R

R

R

D

L

L

A

V

G

D

A

D

I

I

-

F

T

T

V

V

S

T

D

E

G

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

F

L

A

V

F
x
W

R

E

H

R

L

M

K

K

I

L

V
x
L

L

I

E
|
E

P

P

G
x
T

G

A

A

G

V

V

S

G

L

V

A

A

L

V

L

L

A

S

G

Q

K

H

I

F

G

Q

T

T

-

V

-

S

-

P

K

E

G

V

R

K

T

N

T

I

A

C

M

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V
|
V

D

D

P
x
L

T

T

active site: K53 (= K55), S81 (= S80), E207 (= E207), A211 (≠ F211), D213 (= D213), G236 (≠ A236), L309 (= L306), S310 (= S307)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (= D213)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F272), L278 (≠ V278), V314 (= V311), L316 (≠ P313)
binding magnesium ion: N244 (≠ L245)
binding pyridoxal-5'-phosphate: F52 (= F54), K53 (= K55), N83 (= N82), G182 (≠ S182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), E280 (= E280), T282 (≠ G282), S310 (= S307), G311 (= G308)

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)
36% identity, 89% coverage: 25:314/326 of query aligns to 23:317/323 of 7nbcCCC

query
sites
7nbcCCC

T

T

P

P

L

V

L

L

E

T

S

S

P

S

A

I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A
x
T

F
x
H

S

S

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K

K

V

K

E

L

G

A

V

I

I

Q

G

A

F

Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E

S

S

R

R

E

E

A

N

I

V

G

A

A

K

A

R

I

V

A

T

A

E

E

E

R

T

G

E

S

G

I

I

L

M

V
|
V

P
x
H

P
|
P

F

N

D

Q

D

E

P

P

F

A

I

V

V

I

E

A

G

G

Q

Q

G

G

T

T

T

I

A

A

L

L

E

E

M

V

L

L

D

N

Q

Q

A

V

D

P

A

L

P

-

F

V

D

D

Q

A

L

L

L

V

C

V

G

P

A

V

S
x
G

G
|
G

L
x
M

M

L

A

A

G

G

I

I

N

A

L

I

V

T

M

V

A

K

E

A

R

L

S

K

P

P

A

S

T

V

K

K

V

V

F

Y

V

A

E
|
E

P

P

E

S

A

N

F
x
A

D

D

D
|
D

T

C

A

Y

R

Q

S

S

L

K

A

L

A

K

G

G

E

K

R

L

V

M

G

P

H

N

P

L

Q

Y

G

P

A

P

P

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

M

K

S

S

P

S

M

I

P

-

G

G

V

L

L

N

T

T

W

W

P

P

I

I

N

I

R

R

R

D

L

L

A

V

G

D

A

D

I

I

-

F

T

T

V

V

S

T

D

E

G

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

F

L

A

V

F

W

R

E

H

R

L

M

K

K

I

L

V

L

L

I

E

E

P

P

G
x
T

G

A

A

G

V

V

S

G

L

V

A

A

L

V

L

L

A

S

G

Q

K

H

I

F

G

Q

T

T

-

V

-

S

-

P

K

E

G

V

R

K

T

N

T

I

A

C

M

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

L

T

T

active site: K53 (= K55), S81 (= S80), E207 (= E207), A211 (≠ F211), D213 (= D213), G236 (≠ A236), L309 (= L306), S310 (= S307)
binding biphenyl-4-ylacetic acid: T78 (≠ A77), H79 (≠ F78), H84 (= H83), V148 (= V147), H149 (≠ P148), P150 (= P149)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (= D213)
binding pyridoxal-5'-phosphate: F52 (= F54), K53 (= K55), N83 (= N82), G182 (≠ S182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G282), S310 (= S307), G311 (= G308)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
36% identity, 89% coverage: 25:314/326 of query aligns to 23:317/323 of 7nbcAAA

query
sites
7nbcAAA

T

T

P

P

L

V

L

L

E

T

S

S

P

S

A

I

L

L

N

N

A

Q

V

L

V

T

G

G

G

R

R

N

V

L

M

F

K

K

A

C

E

E

S

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

I

V

S

R

R

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

E

R

K

K

A

P

R

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

A

Y

A

A

A

K

M

L

V

E

G

G

T

I

P

P

A

A

I

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

R

D

V

C

K

K

V

K

E

L

G

A

V

I

I

Q

G

A

F

Y

G

G

G

A

E

S

V

I

R

V

F

Y

Y

C

D

E

R

P

W

S

T

D

E

E