SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_017557702.1 NCBI__GCF_000341205.1:WP_017557702.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

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)
30% identity, 91% coverage: 20:322/334 of query aligns to 8:311/323 of O59791

query
sites
O59791

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N

K57 (= K69) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ T94) 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 (= N96) binding pyridoxal 5'-phosphate
G183 (= G195) binding pyridoxal 5'-phosphate
G184 (= G196) binding pyridoxal 5'-phosphate
G185 (= G197) binding pyridoxal 5'-phosphate
G186 (≠ S198) binding pyridoxal 5'-phosphate
L187 (≠ G199) binding pyridoxal 5'-phosphate
E208 (≠ Q220) binding Mg(2+)
G212 (≠ S224) binding Mg(2+)
D214 (≠ A226) binding Mg(2+)
S308 (≠ T319) binding pyridoxal 5'-phosphate

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
30% identity, 91% coverage: 20:322/334 of query aligns to 4:307/319 of 2zr8A

query
sites
2zr8A

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active site: K53 (= K69), S78 (≠ T94), E204 (≠ Q220), G208 (≠ S224), D210 (≠ A226), G232 (= G247), I303 (≠ C318), S304 (≠ T319)
binding magnesium ion: E204 (≠ Q220), G208 (≠ S224), D210 (≠ A226)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F68), K53 (= K69), S77 (= S93), S78 (≠ T94), N80 (= N96), H81 (= H97), P147 (= P163), G179 (= G195), G180 (= G196), G181 (= G197), G182 (≠ S198), G232 (= G247), E277 (= E292), T279 (≠ A294), S304 (≠ T319)
binding serine: S78 (≠ T94), R129 (≠ A145), D231 (≠ E246), G232 (= G247), A233 (≠ L248), Q234 (≠ A249), T235 (= T250)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
30% identity, 91% coverage: 20:322/334 of query aligns to 4:307/319 of 2zpuA

query
sites
2zpuA

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N

active site: K53 (= K69), S78 (≠ T94), E204 (≠ Q220), G208 (≠ S224), D210 (≠ A226), G232 (= G247), I303 (≠ C318), S304 (≠ T319)
binding magnesium ion: E204 (≠ Q220), G208 (≠ S224), D210 (≠ A226)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F68), K53 (= K69), S77 (= S93), S78 (≠ T94), N80 (= N96), H81 (= H97), P147 (= P163), G179 (= G195), G180 (= G196), G181 (= G197), G182 (≠ S198), G232 (= G247), E277 (= E292), T279 (≠ A294), S304 (≠ T319)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
30% identity, 91% coverage: 20:322/334 of query aligns to 3:306/318 of 1wtcA

query
sites
1wtcA

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L

Y

P

T

Q

F

S

S

V

I

M

I

R

K

G

E

R

K

L

V

D

D

F

I

V

L

L

T

V

V

G

S

D

D

E

E

D

E

I

L

R

I

R

D

A

C

Q

L

W

K

W

F

A

Y

L

A

S

A

E

R

A

M

R

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

A

S

L

F

A

A

G

A

A

A

Y

R

A

A

L

M

R

K

A

E

D

K

L

L

R

K

D

N

L

K

R

R

V

I

A

G

V

I

C
x
I

T
x
S

G

G

A

G

N

N

active site: K52 (= K69), S77 (≠ T94), E203 (≠ Q220), G207 (≠ S224), D209 (≠ A226), G231 (= G247), I302 (≠ C318), S303 (≠ T319)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ E37), K47 (≠ P64), M48 (≠ T65), A109 (≠ E126), A110 (= A127), Y114 (≠ L131)
binding magnesium ion: E203 (≠ Q220), G207 (≠ S224), D209 (≠ A226)
binding pyridoxal-5'-phosphate: F51 (= F68), K52 (= K69), N79 (= N96), G178 (= G195), G179 (= G196), G180 (= G197), G181 (≠ S198), G231 (= G247), E276 (= E292), T278 (≠ A294), S303 (≠ T319)

1v71A Crystal structure of s.Pombe serine racemase
30% identity, 91% coverage: 20:322/334 of query aligns to 3:306/318 of 1v71A

query
sites
1v71A

P

P

D

T

I

Y

T

D

D

D

V

V

L

A

R

S

A

A

R

S

R

E

L

R

L

I

Q

K

G

K

R

F

L

A

E

N

P

K

T

T

P

P

L

V

R

L

S

T

Y

S

P

S

A

T

L

V

D

N

R

K

R

E

I

F

G

V

A

A

R

E

V

V

L

F

V

F

K

K

H

C

E

E

N

N

T

F

Q

Q

P

K

T

M

G

G

A

A

F
|
F

K
|
K

V

F

R

R

G

G

G

A

L

L

V

N

L

A

L

L

A

S

G

Q

M

L

S

N

R

E

E

A

E

Q

R

R

S

K

R

A

G

G

V

V

V

L

T

T

Y

F

S

S

T
x
S

G

G

N
|
N

H

H

A

A

Q

Q

S

A

I

I

A

A

Y

L

A

S

A

A

R

K

E

I

T

L

G

G

A

I

P

P

C

A

A

K

I

I

V

I

V

M

P

P

E

L

N

D

P

A

N

P

P

E

V

A

K

K

A

V

E

A

A

A

I

T

R

K

A

G

L

Y

G

G

A

G

D

Q

L

V

V

I

E

M

A

Y

G

D

A

R

D

Y

L

K

D

D

G

D

A

R

R

E

E

K

R

M

A

A

E

K

A

E

L

I

A

S

A

E

E

R

R

E

G

G

A

L

R

T

L

I

V

I

S

P

P

P

G

Y

D

D

E

H

P

P

D

H

L

V

I

L

A

A

G

G

V

Q

A

G

T

T

A

A

Y

A

L

K

E

E

L

L

F

F

E

E

Q

E

A

V

P

G

D

P

L

L

D

D

A

A

V

L

V

F

V

V

P

C

V

L

G
|
G

S
x
G

G

L

A

L

A

S

A

G

A

S

C

A

I

L

S

A

A

A

A

R

A

H

V

F

A

A

P

P

G

N

C

C

R

E

V

V

V

Y

G

G

A

V

Q
x
E

S

P

S

E

A

A

S
x
G

P

N

A
x
D

A

G

H

Q

D

Q

S

S

W

F

R

R

A

K

G

G

S

S

C

I

T

V

-

H

V

I

R

D

P

T

N

P

R

K

T

T

R

I

A

A

E

D

G
|
G

L

A

A

Q

T

T

G

Q

R

H

G

L

F

G

A

N

L

Y

P

T

Q

F

S

S

V

I

M

I

R

K

G

E

R

K

L

V

D

D

F

I

V

L

L

T

V

V

G

S

D

D

E

E

D

E

I

L

R

I

R

D

A

C

Q

L

W

K

W

F

A

Y

L

A

S

A

E

R

A

M

R

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

A

S

L

F

A

A

G

A

A

A

Y

R

A

A

L

M

R

K

A

E

D

K

L

L

R

K

D

N

L

K

R

R

V

I

A

G

V

I

C
x
I

T
x
S

G
|
G

A

G

N

N

active site: K52 (= K69), S77 (≠ T94), E203 (≠ Q220), G207 (≠ S224), D209 (≠ A226), G231 (= G247), I302 (≠ C318), S303 (≠ T319)
binding magnesium ion: E203 (≠ Q220), G207 (≠ S224), D209 (≠ A226)
binding pyridoxal-5'-phosphate: F51 (= F68), K52 (= K69), N79 (= N96), G178 (= G195), G179 (= G196), G180 (= G197), G181 (≠ S198), G231 (= G247), E276 (= E292), T278 (≠ A294), S303 (≠ T319), G304 (= G320)

P04968 L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 from Escherichia coli (strain K12) (see paper)
35% identity, 87% coverage: 39:329/334 of query aligns to 32:325/514 of P04968

query
sites
P04968

T

T

P

P

L

L

R

Q

S

K

Y

M

P

E

A

K

L

L

D

S

R

S

R

R

I

L

G

D

A

N

R

V

V

I

L

L

V

V

K

K

H

R

E

E

N

D

T

R

Q

Q

P

P

T

V

G

H

A

S

F

F

K
|
K

V

L

R

R

G

G

G

A

L

Y

V

A

L

M

A

A

G

G

M

L

S

T

R

E

E

E

E

Q

R

K

S

A

R

H

G

G

V

V

V

I

T

T

Y

A

S

S

T

A

G

G

N
|
N

H

H

A

A

Q

Q

S

G

I

V

A

A

Y

F

A

S

R

A

E

R

T

L

G

G

A

V

P

K

C

A

A

L

I

I

V

V

V

M

P

P

E

T

N

A

P

T

N

A

P

D

V

I

K

K

A

V

E

D

A

A

I

V

R

R

A

G

L

F

G

G

A

G

D

E

L

V

V

L

E

L

A

H

G

G

A

A

D

N

L

F

D

D

G

E

A

A

R

K

E

A

R

K

A

A

E

I

A

E

L

L

A

S

A

Q

E

Q

R

Q

G

G

A

F

R

T

L

W

V

V

S

P

P

P

G

F

D

D

E

H

P

P

D

M

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

L

Y

A

L

L

E

E

L

L

F

L

E

Q

Q

Q

A

D

P

A

D

H

L

L

D

D

A

R

V

V

V

F

V

V

P

P

V

V

G
|
G

S
x
G

G
x
L

A

A

A

G

A

V

C

A

I

V

S

L

A

I

A

K

A

Q

V

L

A

M

P

P

G

Q

C

I

R

K

V

V

V

I

G

A

A

V

Q

E

S

A

S

E

A

D

S

S

P

A

A

C

A

L

H

K

D

A

S

A

W

L

R

D

A

A

G

G

S

H

C

P

T

V

V

D

R

L

P

P

N

R

R

V

-

G

T

L

R

F

A

A

E

E

G

G

L

V

A

A

T

V

G

K

R

R

-

I

-

G

-

D

-

E

G

T

F

F

A

R

L

L

P

C

Q

Q

S

E

V

Y

M

-

R

-

G

-

R

-

L

L

D

D

F

I

V

I

L

T

V

V

G

D

D

S

E

D

D

A

I

I

R

C

R

A

A

A

Q

M

W

K

W

D

A

L

L

F

S

E

E

D

A

V

R

R

T

A

V

V

A

A

E

E

G

P

A

S

G

G

A

A

A

L

A

A

L

L

A

A

G

G

-

M

-

K

A

K

Y

Y

A

I

L

A

R

L

A

H

D

N

L

I

R

R

D

G

L

E

R

R

V

L

A

A

V

H

V

I

C

L

T
x
S

G

G

A

A

N

N

A

V

A

N

P

F

D

H

E

G

L

L

R

R

K62 (= K69) modified: N6-(pyridoxal phosphate)lysine
N89 (= N96) binding pyridoxal 5'-phosphate
GGGGL 188:192 (≠ GGGSG 195:199) binding pyridoxal 5'-phosphate
S315 (≠ T319) binding pyridoxal 5'-phosphate

1tdjA Threonine deaminase (biosynthetic) from e. Coli (see paper)
35% identity, 87% coverage: 39:329/334 of query aligns to 28:321/494 of 1tdjA

query
sites
1tdjA

T

T

P

P

L

L

R

Q

S

K

Y

M

P

E

A

K

L

L

D

S

R

S

R

R

I

L

G

D

A

N

R

V

V

I

L

L

V

V

K

K

H

R

E

E

N

D

T

R

Q

Q

P

P

T

V

G

H

A

S

F
|
F

K
|
K

V

L

R

R

G

G

G

A

L

Y

V

A

L

M

A

A

G

G

M

L

S

T

R

E

E

E

E

Q

R

K

S

A

R

H

G

G

V

V

V

I

T

T

Y

A

S

S

T
x
A

G

G

N
|
N

H

H

A

A

Q

Q

S

G

I

V

A

A

Y

F

A

S

R

A

E

R

T

L

G

G

A

V

P

K

C

A

A

L

I

I

V

V

V

M

P

P

E

T

N

A

P

T

N

A

P

D

V

I

K

K

A

V

E

D

A

A

I

V

R

R

A

G

L

F

G

G

A

G

D

E

L

V

V

L

E

L

A

H

G

G

A

A

D

N

L

F

D

D

G

E

A

A

R

K

E

A

R

K

A

A

E

I

A

E

L

L

A

S

A

Q

E

Q

R

Q

G

G

A

F

R

T

L

W

V

V

S

P

P

P

G

F

D

D

E

H

P

P

D

M

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

L

Y

A

L

L

E

E

L

L

F

L

E

Q

Q

Q

A

D

P

A

D

H

L

L

D

D

A

R

V

V

V

F

V

V

P

P

V

V

G
|
G

S
x
G

G

L

A

A

A

G

A

V

C

A

I

V

S

L

A

I

A

K

A

Q

V

L

A

M

P

P

G

Q

C

I

R

K

V

V

V

I

G

A

A

V

Q
x
E

S

A

S

E

A

D

S
|
S

P

A

A
x
C

A

L

H

K

D

A

S

A

W

L

R

D

A

A

G

G

S

H

C

P

T

V

V

D

R

L

P

P

N

R

R

V

-

G

T

L

R

F

A

A

E

E

G
|
G

L

V

A

A

T

V

G

K

R

R

-

I

-

G

-

D

-

E

G

T

F

F

A

R

L

L

P

C

Q

Q

S

E

V

Y

M

-

R

-

G

-

R

-

L

L

D

D

F

I

V

I

L

T

V

V

G

D

D

S

E

D

D

A

I

I

R

C

R

A

A

A

Q

M

W

K

W

D

A

L

L

F

S

E

E

D

A

V

R

R

T

A

V

V

A

A

E
|
E

G

P

A

S

G

G

A

A

A

L

A

A

L

L

A

A

G

G

-

M

-

K

A

K

Y

Y

A

I

L

A

R

L

A

H

D

N

L

I

R

R

D

G

L

E

R

R

V

L

A

A

V

H

V

I

C
x
L

T
x
S

G
|
G

A

A

N

N

A

V

A

N

P

F

D

H

E

G

L

L

R

R

active site: K58 (= K69), A83 (≠ T94), E209 (≠ Q220), S213 (= S224), C215 (≠ A226), G237 (= G247), L310 (≠ C318), S311 (≠ T319)
binding pyridoxal-5'-phosphate: F57 (= F68), K58 (= K69), N85 (= N96), G184 (= G195), G185 (= G196), G186 (= G197), G187 (≠ S198), G237 (= G247), E282 (= E292), S311 (≠ T319), G312 (= G320)

8y1jA Structure of the pyridoxal 5'-phosphate-dependent (plp) threonine deaminase ilva1 from pseudomonas aeruginosa pao1 (see paper)
34% identity, 87% coverage: 39:329/334 of query aligns to 20:314/502 of 8y1jA

query
sites
8y1jA

T

T

P

P

L

L

R

Q

S

P

Y

A

P

R

A

Q

L

L

D

S

R

E

R

R

I

L

G

G

A

N

R

Q

V

V

L

L

V

L

K

K

H

R

E

E

N

D

T

L

Q

Q

P

P

T

V

G

F

A

S

F

F

K
|
K

V

I

R

R

G

G

G

A

L

Y

V

N

L

K

L

V

A

A

G

Q

M

L

S

T

R

E

E

E

R

K

S

A

R

R

G

G

V

V

V

I

T

A

Y

A

S
|
S

T

A

G

G

N

N

H
|
H

A

A

Q

Q

S

G

I

L

A

A

Y

L

A

A

R

K

E

R

T

Q

G

G

A

I

P

R

C

A

A

V

I

I

V

V

V

M

P

P

E

K

N

T

P

T

N

P

P

E

V

I

K

K

A

V

E

Q

A

A

I

V

R

R

A

A

L

H

G

G

A

A

D

K

L

A

V

V

E

L

A

H

G

G

A

D

D

A

L

F

D

P

G

E

A

A

R

L

E

A

R

H

A

A

E

L

A

K

L

L

A

V

A

D

E

E

R

K

G

G

A

Y

R

T

L

F

V

V

S

H

P

P

G

Y

D

D

E

D

P

P

D

D

L

T

I

I

A

A

G

G

V

Q

A

G

T

T

A

V

Y

A

L

M

E

E

L

I

F

L

E

R

Q

Q

A

Q

P

P

D

G

-

R

L

L

D

D

A

A

V

I

V

F

V

V

P

P

V

V

G

G

S

G

G

L

A

V

A

A

A

G

A

I

C

A

I

A

S

Y

A

V

A

K

A

Y

V

L

A

R

P

P

G

E

C

I

R

K

V

V

V

I

G

G

A

V

Q

E

S

P

S

D

A

E

S

S

P

N

A

C

A

L

H

Q

D

A

S

A

W

M

R

A

A

A

G

G

S

E

C

R

T

V

V

V

R

L

P

G

N

Q

R

V

-

G

T

L

R

F

A

A

E

D

G

G

L

V

A

A

T

V

G

A

R

Q

G

I

F

G

A

Q

L

H

P

T

Q

F

S

D

V

I

M

C

R

K

G

D

R

H

L

V

D

D

D

E

F

V

V

I

L

T

V

V

G

S

D

T

E

D

D

E

I

I

R

C

R

A

A

A

Q

I

W

K

W

D

A

I

L

Y

S

D

E

D

A

T

R

R

T

S

V

I

A

T

E

E

G

P

A

A

G

G

A

A

A

L

A

A

L

V

A

A

G

G

-

I

-

K

A

K

Y

Y

A

V

L

E

R

R

A

E

D

R

L

A

R

E

D

G

L

Q

R

T

V

L

A

V

V

A

V

I

C

D

T

S

G

G

A

A

N

N

A

V

A

N

P

F

D

D

E

R

L

L

R

R

binding 2-ketobutyric acid: K50 (= K69), S74 (= S93), H78 (= H97)

Sites not aligning to the query:

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

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)
32% identity, 93% coverage: 24:332/334 of query aligns to 8:317/319 of A4F2N8

query
sites
A4F2N8

D

D

V

V

L

I

R

K

A

A

R

A

R

E

L

R

L

L

Q

E

G

G

R

F

L

A

E

N

P

R

T

T

P

P

L

V

R

F

S

T

Y

S

P

R

A

T

L

L

D

D

R

A

R

E

I

T

G

G

A

A

R

Q

V

V

L

F

V

I

K

K

H

C

E

E

N

N

T

L

Q

Q

P

R

T

T

G

G

A

S

F

F

K
|
K

V

F

R

R

G

G

G

A

L

F

V

N

L

A

L

L

A

S

G

R

M

F

S

D

R

E

E

A

E

Q

R

R

S

K

R

A

G

G

V

V

T

A

Y

F

S

S

T

S

G

G

N

N

H

H

A

A

Q

Q

S

G

I

I

A

A

Y

L

A

A

R

R

E

L

T

L

G

Q

A

M

P

P

C

A

A

T

I

I

V

V

V

M

P

P

E

T

N

D

P

A

N

P

P

A

V

A

K

K

A

V

E

A

A

A

I

T

R

R

A

E

L

Y

G

G

A

A

D

T

L

V

V

V

E

F

A

Y

G

D

A

R

D

I

L

T

D

E

G

D

A

R

R

E

E

Q

R

I

A

G

E

R

A

T

L

L

A

A

A

E

E

Q

R

H

G

G

A

M

R

T

L

L

V

I

S

P

P

S

G

Y

D

D

E

H

P

P

D

D

L

V

I

L

A

A

G

G

V

Q

A

G

T

T

A

A

Y

A

L

K

E

E

L

L

F

L

E

E

Q

F

A

T

P

G

D

P

L

L

D

D

A

A

V

L

V

F

V

V

P

G

V

L

G

G

S

G

G

M

A

L

A

S

A

G

A

T

C

A

I

L

S

A

A

T

A

R

A

A

V

L

A

S

P

P

G

D

C

C

R

L

V

L

V

Y

G

G

A

V

Q

E

S

P

S

E

A

A

S

G

P

N

A

D

A

G

H

Q

D

R

S

S

W

F

R

Q

A

T

G

G

S

S

C

I

T

V

-

H

V

I

R

D

P

T

N

P

R

A

T

T

R

I

A

A

E

D

G

G

L

A

A

Q

T

T

G

Q

R

H

G

L

F

G

A

N

L

H

P

T

Q

F

S

P

V

I

M

I

R

R

G

E

R

N

L

V

D

N

D

D

F

I

V

L

L

T

V

V

G

S

D

D

E

A

D

E

I

L

R

V

R

E

A

S

Q

M

W

R

W

F

A

F

L

M

S

Q

E

R

A

M

R

K

T

M

V

V

A

V

E

E

G

P

A

T

G

G

A

C

A

L

A

G

L

L

A

A

G

A

A

L

Y

R

A

N

L

L

R

K

A

Q

D

Q

L

F

R

R

D

G

L

Q

R

R

V

V

A

G

V

I

C

V

T

T

G

G

A

G

N

N

A

V

A

D

P

I

D

E

E

K

L

Y

R

A

G

S

L

L

K53 (= K69) mutation to A: Loss of enzymatic activity.

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
30% identity, 90% coverage: 24:323/334 of query aligns to 9:310/322 of 3l6bA

query
sites
3l6bA

D

D

V

V

L

E

R

K

A

A

R

H

R

I

L

N

L

I

Q

R

G

D

R

S

L

I

E

H

P

L

T

T

P

P

L

V

R

L

S

T

Y

S

P

S

A

I

L

L

D

N

R

Q

R

L

I

T

G

G

A

R

R

N

V

L

L

F

V

F

K

K

H

C

E

E

N

L

T

F

Q

Q

P

K

T

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

G

A

L

L

V

N

L

A

L

V

A

R

G

S

M

L

S

V

R

R

E

-

R

K

S

P

R

K

G

A

V

V

T

T

Y

H

S
|
S

T
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

S

A

I

L

A

T

Y

Y

A

A

R

K

E

L

T

E

G

G

A

I

P

P

C

A

A

Y

I

I

V

V

P

P

E

Q

N

T

P

A

N

P

P

D

V

C

K

K

A

K

E

L

A

A

I

I

R

Q

A

A

L

Y

G

G

A

A

D

S

L

I

V

V

E

Y

A

C

G

E

A

P

D

S

L

D

D

E

G

S

A
x
R

R

E

E

N

R

V

A

A

E

K

A

R

L

V

A

T

A

E

E

E

R

T

G

E

A

G

R

I

L

M

V

V

S

H

P

P

G

N

D

Q

E

E

P

P

D

A

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

I

Y

A

L

L

E

E

L

V

F

L

E

N

Q

Q

A

V

P

P

D

L

L

V

D

D

A

A

V

L

V

V

P

P

V

V

G
|
G

S
x
G

G
x
M

A

L

A

A

A

G

A

I

C

A

I

I

S

T

A

V

A

K

A

A

V

L

A

K

P

P

G

S

C

V

R

K

V

V

V

Y

G

A

A

A

Q
x
E

S

P

S

S

A

N

S
x
A

P

D

A
x
D

A

C

H

Y

D

Q

S

S

W

K

R

L

A

K

G

G

S

K

C

L

-

M

-

P

T

N

V

L

R

Y

P

P

N

P

R

E

T

T

R

I

A

A

E

D

G
|
G

L
x
V

A

K

T

S

G

S

R

I

G

G

F

L

A

N

L

-

P

T

Q

W

S

P

V

I

M

I

R

R

G

D

R

L

L

V

D

D

F

I

V

F

L

T

V

V

G

T

D

E

E

D

D

E

I

I

R

K

R

C

A

A

Q

T

W

Q

W

L

A

V

L

W

S

E

E

R

A

M

R

K

T

L

V

L

A

I

E
|
E

-

P

-
x
T

-

A

G

G

A

V

G

G

A

V

A

A

L

V

A

L

G

S

A

Q

Y

H

A

F

L

Q

R

T

A

V

D

S

L

P

R

E

D

V

L

K

R

N

V

I

A

C

V

I

V

V

C
x
L

T
x
S

G
|
G

A

G

N

N

A

V

active site: K54 (= K69), S77 (≠ T94), E203 (≠ Q220), A207 (≠ S224), D209 (≠ A226), G232 (= G247), T278 (vs. gap), L305 (≠ C318), S306 (≠ T319)
binding malonate ion: K54 (= K69), S76 (= S93), S77 (≠ T94), N79 (= N96), H80 (= H97), R128 (≠ A145), G232 (= G247)
binding manganese (ii) ion: E203 (≠ Q220), A207 (≠ S224), D209 (≠ A226)
binding pyridoxal-5'-phosphate: F53 (= F68), K54 (= K69), N79 (= N96), G178 (= G195), G179 (= G196), G180 (= G197), G181 (≠ S198), M182 (≠ G199), V233 (≠ L248), E276 (= E292), T278 (vs. gap), S306 (≠ T319), G307 (= G320)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
30% identity, 90% coverage: 24:323/334 of query aligns to 8:309/310 of 7nbgDDD

query
sites
7nbgDDD

D

D

V

V

L

E

R

K

A

A

R

H

R

I

L

N

L

I

Q

R

G

D

R

S

L

I

E

H

P

L

T

T

P

P

L

V

R

L

S

T

Y

S

P

S

A

I

L

L

D

N

R

Q

R

L

I

T

G

G

A

R

R

N

V

L

L

F

V

F

K

K

H

C

E

E

N

L

T

F

Q

Q

P

K

T

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

G

A

L

L

V

N

L

A

L

V

A

R

G

S

M

L

S

V

R

R

E

-

R

K

S

P

R

K

G

A

V

V

T

T

Y

H

S

S

T
x
S

G

G

N
|
N

H

H

A

G

Q
|
Q

S

A

I

L

A

T

Y

Y

A

A

R

K

E

L

T

E

G

G

A

I

P

P

C

A

A

Y

I
|
I

V

V

P

P

E

Q

N

T

P

A

N

P

P

D

V

C

K

K

A

K

E

L

A

A

I

I

R

Q

A

A

L
x
Y

G

G

A

A

D

S

L

I

V

V

E

Y

A

C

G

E

A

P

D

S

L

D

D

E

G

S

A

R

R

E

E

N

R

V

A

A

E

K

A

R

L

V

A

T

A

E

E

E

R

T

G

E

A

G

R

I

L

M

V

V

S

H

P

P

G

N

D

Q

E

E

P

P

D

A

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

I

Y

A

L

L

E

E

L

V

F

L

E

N

Q

Q

A

V

P

P

D

L

L

V

D

D

A

A

V

L

V

V

P

P

V

V

G
|
G

S
x
G

G
x
M

A

L

A

A

A

G

A

I

C

A

I

I

S

T

A

V

A

K

A

A

V

L

A

K

P

P

G

S

C

V

R

K

V

V

V

Y

G

A

A

A

Q
x
E

S

P

S

S

A

N

S
x
A

P

D

A
x
D

A

C

H

Y

D

Q

S

S

W

K

R

L

A

K

G

G

S

K

C

L

-

M

-

P

T

N

V

L

R

Y

P

P

N

P

R

E

T

T

R

I

A

A

E

D

G
|
G

L
x
V

A

K

T

S

G

S

R

I

G

G

F

L

A
x
N

L

-

P

T

Q

W

S

P

V

I

M

I

R

R

G

D

R

L

L

V

D

D

F

I

V

F

L

T

V

V

G

T

D

E

E

D

D

E

I

I

R

K

R

C

A

A

Q

T

W

Q

W

L

A

V

L

W

S

E

E

R

A

M

R

K

T

L

V

L

A

I

E
|
E

-

P

-
x
T

-

A

G

G

A

V

G

G

A

V

A

A

L

V

A

L

G

S

A

Q

Y

H

A

F

L

Q

R

T

A

V

D

S

L

P

R

E

D

V

L

K

R

N

V

I

A

C

V

I

V

V

C
x
L

T
x
S

G
|
G

A

G

N

N

A

V

active site: K53 (= K69), S76 (≠ T94), E202 (≠ Q220), A206 (≠ S224), D208 (≠ A226), G231 (= G247), L304 (≠ C318), S305 (≠ T319)
binding calcium ion: E202 (≠ Q220), A206 (≠ S224), D208 (≠ A226)
binding magnesium ion: N239 (≠ A255)
binding ortho-xylene: S76 (≠ T94), Q81 (= Q99), I96 (= I114), Y113 (≠ L131)
binding pyridoxal-5'-phosphate: F52 (= F68), K53 (= K69), N78 (= N96), G177 (= G195), G178 (= G196), G179 (= G197), G180 (≠ S198), M181 (≠ G199), G231 (= G247), V232 (≠ L248), E275 (= E292), T277 (vs. gap), S305 (≠ T319), G306 (= G320)

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)
30% identity, 90% coverage: 24:323/334 of query aligns to 8:314/322 of 7nbgAAA

query
sites
7nbgAAA

D

D

V

V

L

E

R

K

A

A

R

H

R

I

L

N

L

I

Q

R

G

D

R

S

L

I

E

H

P

L

T

T

P

P

L

V

R

L

S

T

Y

S

P

S

A

I

L

L

D

N

R

Q

R

L

I

T

G

G

A

R

R

N

V

L

L

F

V

F

K

K

H

C

E

E

N

L

T

F

Q

Q

P

K

T

T

G

G

A

S

F
|
F

K
|
K

V

I

R

R

G

G

G

A

L

L

V

N

L

A

L

V

A

R

G

S

M

L

-

V

-

P

-

D

S

A

R

L

E

E

E

R

R

K

S

P

R

K

G

A

V

V

T

T

Y

H

S

S

T
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

S

A

I

L

A

T

Y

Y

A

A

R

K

E

L

T

E

G

G

A

I

P

P

C

A

A

Y

I
|
I

V

V

P

P

E

Q

N

T

P

A

N

P

P

D

V

C

K
|
K

A

K

E

L

A

A

I
|
I

R

Q

A

A

L
x
Y

G

G

A

A

D

S

L

I

V

V

E

Y

A

C

G

E

A

P

D

S

L

D

D

E

G

S

A

R

R

E

E

N

R

V

A

A

E

K

A

R

L

V

A

T

A

E

E

E

R

T

G

E

A

G

R

I

L

M

V

V

S

H

P

P

G

N

D

Q

E

E

P

P

D

A

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

I

Y

A

L

L

E

E

L

V

F

L

E

N

Q

Q

A

V

P

P

D

L

L

V

D

D

A

A

V

L

V

V

P

P

V

V

G
|
G

S
x
G

G
x
M

A

L

A

A

A

G

A

I

C

A

I

I

S

T

A

V

A

K

A

A

V

L

A

K

P

P

G

S

C

V

R

K

V

V

V

Y

G

A

A

A

Q
x
E

S

P

S

S

A

N

S
x
A

P

D

A
x
D

A

C

H

Y

D

Q

S

S

W

K

R

L

A

K

G

G

S

K

C

L

-

M

-

P

T

N

V

L

R

Y

P

P

N

P

R

E

T

T

R

I

A

A

E

D

G
|
G

L
x
V

A

K

T

S

G

S

R

I

G

G

F

L

A

N

L

-

P

T

Q

W

S

P

V

I

M

I

R

R

G

D

R

L

L

V

D

D

F

I

V

F

L

T

V

V

G

T

D

E

E

D

D

E

I

I

R

K

R

C

A

A

Q

T

W

Q

W

L

A

V

L

W

S

E

E

R

A

M

R

K

T

L

V

L

A

I

E

E

-

P

-
x
T

-

A

G

G

A

V

G

G

A

V

A

A

L

V

A

L

G

S

A

Q

Y

H

A

F

L

Q

R

T

A

V

D

S

L

P

R

E

D

V

L

K

R

N

V

I

A

C

V

I

V

V

C
x
L

T
x
S

G
|
G

A

G

N

N

A

V

active site: K53 (= K69), S81 (≠ T94), E207 (≠ Q220), A211 (≠ S224), D213 (≠ A226), G236 (= G247), L309 (≠ C318), S310 (≠ T319)
binding calcium ion: E207 (≠ Q220), A211 (≠ S224), D213 (≠ A226)
binding pyridoxal-5'-phosphate: F52 (= F68), K53 (= K69), N83 (= N96), G182 (= G195), G183 (= G196), G184 (= G197), G185 (≠ S198), M186 (≠ G199), G236 (= G247), V237 (≠ L248), T282 (vs. gap), S310 (≠ T319), G311 (= G320)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ T94), G85 (≠ A98), Q86 (= Q99), I101 (= I114), K111 (= K124), I115 (= I128), Y118 (≠ L131)

6zspAAA serine racemase bound to atp and malonate. (see paper)
30% identity, 90% coverage: 24:323/334 of query aligns to 8:307/320 of 6zspAAA

query
sites
6zspAAA

D

D

V

V

L

E

R

K

A

A

R

H

R

I

L

N

L

I

Q

R

G

D

R

S

L

I

E

H

P

L

T

T

P

P

L

V

R

L

S

T

Y
x
S

P
x
S

A
x
I

L

L

D

N

R

Q

R

L

I

T

G

G

A

R

R

N

V

L

L

F

V

F

K

K

H

C

E

E

N

L

T

F

Q

Q

P
x
K

T
|
T

G

G

A

S

F

F

K
|
K

V

I

R

R

G

G

G

A

L

L

V

-

L

-

A

-

G

N

M

A

S

V

R

R

E

S

E

L

R

K

S

P

R

K

G

A

V

V

T

T

Y

H

S
|
S

T
x
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

S

A

I

L

A

T

Y

Y

A

A

R

K

E

L

T

E

G

G

A

I

P

P

C

A

A

Y

I

I

V

V

P

P

E

Q

N

T

P

A

N

P

P

D

V

C

K

K

A

K

E

L

A

A

I

I

R

Q

A

A

L
x
Y

G

G

A

A

D

S

L

I

V

V

E

Y

A

C

G

E

A

P

D

S

L

D

D

E

G

S

A
x
R

R

E

E

N

R

V

A

A

E

K

A

R

L

V

A

T

A

E

E

E

R

T

G

E

A

G

R

I

L

M

V

V

S

H

P

P

G

N

D

Q

E

E

P

P

D

A

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

I

Y

A

L

L

E

E

L

V

F

L

E

N

Q

Q

A

V

P

P

D

L

L

V

D

D

A

A

V

L

V

V

P

P

V

V

G

G

S

G

G

M

A

L

A

A

A

G

A

I

C

A

I

I

S

T

A

V

A

K

A

A

V

L

A

K

P

P

G

S

C

V

R

K

V

V

V

Y

G

A

A

A

Q
x
E

S

P

S

S

A

N

S
x
A

P

D

A
x
D

A

C

H

Y

D

Q

S

S

W

K

R

L

A

K

G

G

S

K

C

L

-

M

-

P

T

N

V

L

R

Y

P

P

N

P

R

E

T

T

R

I

A

A

E

D

G
|
G

L

V

A

K

T
x
S

G

S

R

I

G

G

F

L

A

N

L

-

P

T

Q

W

S

P

V

I

M

I

R

R

G

D

R

L

L

V

D

D

F

I

V

F

L

T

V

V

G

T

D

E

E

D

D

E

I

I

R

K

R

C

A

A

Q

T

W

Q

W

L

A

V

L

W

S
x
E

E
x
R

A

M

R
x
K

T

L

V

L

A

I

E

E

-

P

-

T

-

A

G

G

A

V

G

G

A

V

A

A

L

V

A

L

G

S

A

Q

Y

H

A

F

L

Q

R

T

A

V

D

S

L

P

R

E

D

V

L

K

R

N

V

I

A

C

V

I

V

V

C
x
L

T
x
S

G

G

A

G

N
|
N

A

V

active site: K53 (= K69), S74 (≠ T94), E200 (≠ Q220), A204 (≠ S224), D206 (≠ A226), G229 (= G247), L302 (≠ C318), S303 (≠ T319)
binding adenosine-5'-triphosphate: S28 (≠ Y44), S29 (≠ P45), I30 (≠ A46), K48 (≠ P64), T49 (= T65), Q79 (= Q99), Y111 (≠ L131), E266 (≠ S285), R267 (≠ E286), K269 (≠ R288), N306 (= N322)
binding magnesium ion: E200 (≠ Q220), A204 (≠ S224), D206 (≠ A226)
binding malonate ion: K53 (= K69), S73 (= S93), S74 (≠ T94), N76 (= N96), H77 (= H97), R125 (≠ A145), G229 (= G247), S232 (≠ T250)

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
30% identity, 90% coverage: 24:323/334 of query aligns to 8:314/320 of 7nbhAAA

query
sites
7nbhAAA

D

D

V

V

L

E

R

K

A

A

R

H

R

I

L

N

L

I

Q

R

G

D

R

S

L

I

E

H

P

L

T

T

P

P

L

V

R

L

S

T

Y

S

P

S

A

I

L

L

D

N

R

Q

R

L

I

T

G

G

A

R

R

N

V

L

L

F

V

F

K

K

H

C

E

E

N

L

T

F

Q

Q

P

K

T

T

G

G

A

S

F

F

K
|
K

V

I

R

R

G

G

G

A

L

L

V

N

L

A

L

V

A

R

G

S

M

L

-

V

-

P

-

D

S

A

R

L

E

E

E

R

R

K

S

P

R

K

G

A

V

V

T

T

Y

H

S

S

T
x
S

G

G

N

N

H

H

A
x
G

Q
|
Q

S

A

I

L

A

T

Y

Y

A

A

R

K

E

L

T

E

G

G

A

I

P

P

C

A

A

Y

I

I

V

V

P

P

E

Q

N

T

P

A

N

P

P

D

V

C

K
|
K

A

K

E

L

A

A

I
|
I

R

Q

A

A

L
x
Y

G

G

A

A

D

S

L

I

V

V

E

Y

A

C

G

E

A

P

D

S

L

D

D

E

G

S

A

R

R

E

E

N

R

V

A

A

E

K

A

R

L

V

A

T

A

E

E

E

R

T

G

E

A

G

R

I

L

M

V

V

S

H

P

P

G

N

D

Q

E

E

P

P

D

A

L

V

I

I

A

A

G

G

V

Q

A

G

T

T

A

I

Y

A

L

L

E

E

L

V

F

L

E

N

Q

Q

A

V

P

P

D

L

L

V

D

D

A

A

V

L

V

V

P

P

V

V

G

G

S

G

G

M

A

L

A

A

A

G

A

I

C

A

I

I

S

T

A

V

A

K

A

A

V

L

A

K

P

P

G

S

C

V

R

K

V

V

V

Y

G

A

A

A

Q
x
E

S

P

S

S

A

N

S
x
A

P

D