SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing Ac3H11_2427 FitnessBrowser__acidovorax_3H11:Ac3H11_2427 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 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
57% identity, 98% coverage: 6:333/334 of query aligns to 1:322/323 of O59791

query
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O59791

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S82 (≠ A87) mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase activity.

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
58% identity, 96% coverage: 12:333/334 of query aligns to 3:318/319 of 2zr8A

query
sites
2zr8A

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active site: K53 (= K62), S78 (≠ A87), E204 (= E213), G208 (≠ A217), D210 (= D219), G232 (= G241), I303 (≠ V318), S304 (= S319)
binding magnesium ion: E204 (= E213), G208 (≠ A217), D210 (= D219)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F61), K53 (= K62), S77 (= S86), S78 (≠ A87), N80 (= N89), H81 (= H90), P147 (= P156), G179 (= G188), G180 (= G189), G181 (= G190), G182 (= G191), G232 (= G241), E277 (= E286), T279 (= T288), S304 (= S319)
binding serine: S78 (≠ A87), R129 (= R138), D231 (= D240), G232 (= G241), A233 (= A242), Q234 (= Q243), T235 (≠ A244)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
58% identity, 96% coverage: 12:333/334 of query aligns to 3:318/319 of 2zpuA

query
sites
2zpuA

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active site: K53 (= K62), S78 (≠ A87), E204 (= E213), G208 (≠ A217), D210 (= D219), G232 (= G241), I303 (≠ V318), S304 (= S319)
binding magnesium ion: E204 (= E213), G208 (≠ A217), D210 (= D219)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F61), K53 (= K62), S77 (= S86), S78 (≠ A87), N80 (= N89), H81 (= H90), P147 (= P156), G179 (= G188), G180 (= G189), G181 (= G190), G182 (= G191), G232 (= G241), E277 (= E286), T279 (= T288), S304 (= S319)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
58% identity, 96% coverage: 12:333/334 of query aligns to 2:317/318 of 1wtcA

query
sites
1wtcA

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P

P

T
|
T

G

G

A

C

L

L

A

S

F

F

A

A

G

A

V

A

Q

R

A

A

F

M

S

K

G

E

E

K

D

-

G

-

A

-

K

-

L

-

L

L

Q

K

G

N

E

K

H

R

V

I

G

G

V

I

I

I

V
x
I

S
|
S

G

G

N

N

V

V

D

D

L

I

P

E

R

R

L

Y

A

A

R

H

F

F

L

L

A

S

active site: K52 (= K62), S77 (≠ A87), E203 (= E213), G207 (≠ A217), D209 (= D219), G231 (= G241), I302 (≠ V318), S303 (= S319)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ H30), K47 (≠ R57), M48 (≠ T58), A109 (= A119), A110 (= A120), Y114 (= Y124)
binding magnesium ion: E203 (= E213), G207 (≠ A217), D209 (= D219)
binding pyridoxal-5'-phosphate: F51 (= F61), K52 (= K62), N79 (= N89), G178 (= G188), G179 (= G189), G180 (= G190), G181 (= G191), G231 (= G241), E276 (= E286), T278 (= T288), S303 (= S319)

1v71A Crystal structure of s.Pombe serine racemase
58% identity, 96% coverage: 12:333/334 of query aligns to 2:317/318 of 1v71A

query
sites
1v71A

L

L

P

P

T

T

H

Y

D

D

V

V

A

A

A

S

A

A

A

S

R

E

R

R

L

I

A

K

G

K

V

F

A

A

H

N

H

K

T

T

P

P

V

V

M

L

R

T

C

S

N

S

T

T

I

V

D

N

E

K

R

E

L

F

G

V

A

A

K

E

L

V

F

F

K

K

C

C

E

E

N

N

L

F

Q

Q

R

K

T

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

Y

L

N

N

A

A

L

L

A

S

Q

Q

F

L

S

N

D

E

A

A

Q

Q

R

R

E

K

H

A

G

G

V

V

L

L

T

T

F

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

A

A

I

I

A

A

L

L

S

S

A

A

R

K

L

I

L

L

D

G

M

I

P

P

A

A

L

K

V

I

M

M

P

P

E

L

D

D

A

A

A

P

A

E

S

A

K

K

M

V

A

A

T

T

R

K

E

G

Y

Y

G

G

A

G

Q

Q

V

V

V

I

T

M

Y

Y

N

D

R

R

Y

Y

T

K

E

D

D

D

R

R

E

E

A

K

I

M

S

A

R

K

Q

E

L

I

A

S

H

E

E

R

R

E

G

G

M

L

T

T

L

I

I

I

P

P

F

Y

D

D

H

H

P

P

H

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

A

A

L

K

E

E

L

L

L

F

Q

E

E

E

V

V

P

G

D

P

L

L

D

D

Y

A

L

L

F

F

V

V

C

C

L

L

G
|
G

L

L

S

S

G

G

S

S

L

A

L

L

A

A

Q

R

A

H

L

F

A

A

P

P

R

N

C

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

T

A

A
x
G

N

N

D
|
D

A

G

Q

Q

S

S

L

F

R

R

A

K

G

G

H

S

I

I

V

V

R

H

I

I

P

D

N

T

P

P

H

K

T

T

I

I

A

A

D

D

G
|
G

A

A

Q

Q

A

T

P

Q

S

H

L

L

G

G

E

N

L

Y

T

T

Y

F

P

S

I

I

R

K

E

E

H

K

V

V

E

D

D

D

I

I

V

L

T

T

V

V

S

S

D

D

Q

E

L

L

I

I

Q

D

A

C

L

L

R

K

F

F

F

Y

A

A

E

A

R

R

M

M

K

K

V

I

V

V

E
|
E

P

P

T
|
T

G

G

A

C

L

L

A

S

F

F

A

A

G

A

V

A

Q

R

A

A

F

M

S

K

G

E

E

K

D

-

G

-

A

-

K

-

L

-

L

L

Q

K

G

N

E

K

H

R

V

I

G

G

V

I

I

I

V
x
I

S
|
S

G
|
G

G

G

N

N

V

V

D

D

L

I

P

E

R

R

L

Y

A

A

R

H

F

F

L

L

A

S

active site: K52 (= K62), S77 (≠ A87), E203 (= E213), G207 (≠ A217), D209 (= D219), G231 (= G241), I302 (≠ V318), S303 (= S319)
binding magnesium ion: E203 (= E213), G207 (≠ A217), D209 (= D219)
binding pyridoxal-5'-phosphate: F51 (= F61), K52 (= K62), N79 (= N89), G178 (= G188), G179 (= G189), G180 (= G190), G181 (= G191), G231 (= G241), E276 (= E286), T278 (= T288), S303 (= S319), G304 (= G320)

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)
58% identity, 97% coverage: 10:332/334 of query aligns to 1:317/319 of A4F2N8

query
sites
A4F2N8

V

M

S

Q

L

L

P

S

T

S

H

Y

D

H

D

D

V

V

A

I

A

K

A

A

R

E

R

R

L

L

A

E

G

G

V

F

A

A

H

N

H

R

T

T

P

P

V

V

M

F

R

T

C

S

N

R

T

T

I

L

D

D

E

A

R

E

L

T

G

G

A

A

K

Q

L

V

F

F

F

I

K

K

C

C

E

E

N

N

L

L

Q

Q

R

R

T

T

G

G

A

S

F

F

K
|
K

F

F

R

R

G

G

A

A

Y

F

N

N

A

A

L

L

A

S

Q

R

F

F

S

D

D

E

A

A

Q

Q

R

R

E

K

H

A

G

G

V

V

L

V

T

A

F

F

S

S

A

S

G

G

N

N

H

H

A

A

Q

Q

A

G

I

I

A

A

L

L

S

A

A

A

R

R

L

L

D

Q

M

M

P

P

A

A

L

T

V

I

V

V

M

M

P

P

E

T

D

D

A

A

A

P

A

A

S

A

K

K

M

V

A

A

T

T

R

R

E

E

Y

Y

G

G

A

A

Q

T

V

V

T

F

Y

Y

N

D

R

R

Y

I

T

T

E

E

D

D

R

R

E

E

A

Q

I

I

S

G

R

R

Q

T

L

L

A

A

H

E

E

Q

R

H

G

G

M

M

T

T

L

L

I

I

P

P

P

S

F

Y

D

D

H

H

P

P

H

D

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

A

A

L

K

E

E

L

L

Q

E

E

F

V

T

P

G

D

P

L

L

D

D

Y

A

L

L

F

F

V

V

C

G

L

L

G

G

L

M

L

L

S

S

G

G

S

T

L

A

L

L

A

A

A

T

Q

R

A

A

L

L

A

S

P

P

R

D

C

C

K

L

V

L

I

Y

G

G

V

V

E

E

P

P

E

E

T

A

A

G

N

N

D

D

A

G

Q

Q

Q

R

S

S

L

F

R

Q

A

T

G

G

H

S

I

I

V

V

R

H

I

I

P

D

N

T

P

P

H

A

T

T

I

I

A

A

D

D

G

G

A

A

Q

Q

A

T

P

Q

S

H

L

L

G

G

E

N

L

H

T

T

Y

F

P

P

I

I

R

R

E

E

H

N

V

V

E

N

D

D

I

I

V

L

T

T

V

V

S

S

D

D

Q

A

Q

E

L

L

I

V

Q

E

A

S

L

M

R

R

F

F

A

M

E

Q

R

R

M

M

K

K

V

M

V

V

E

E

P

P

T

T

G

G

A

C

L

L

A

G

F

L

A

A

G

A

V

L

Q

R

A

N

F

L

S

K

G

Q

E

Q

D

-

G

-

A

-

K

-

L

-

L

F

Q

R

G

G

E

Q

H

R

V

V

G

G

V

I

I

I

V

V

S

T

G

G

N

N

V

V

D

D

L

I

P

E

R

K

L

Y

A

A

R

S

F

L

L

L

K53 (= K62) mutation to A: Loss of enzymatic activity.

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)
42% identity, 93% coverage: 21:332/334 of query aligns to 27:336/339 of Q7XSN8

query
sites
Q7XSN8

A

A

A

Q

R

A

R

R

L

I

A

A

G

P

V

Y

A

V

H

H

H

K

T

T

P

P

V

V

M

L

R

S

C

S

N

T

T

S

I

I

D

D

E

A

R

I

L

V

G

G

A

K

K

Q

L

L

F

F

K

K

C

C

E

E

N

C

L

F

Q

Q

R

K

T

A

G

G

A

A

F

F

K

K

F

I

R

R

G

G

A

A

Y

S

N

N

A

S

L

I

A

F

Q

A

F

L

S

D

D

D

A

D

Q

E

R

A

E

S

H

K

G

G

V

V

L

V

T

T

F

H

S

S

A

S

G

G

N

N

H

H

A

A

Q

A

A

A

I

V

A

A

L

L

S

A

A

A

R

K

L

L

L

R

D

G

M

I

P

P

A

A

L

Y

V

I

V

V

M

I

P

P

E

R

D

N

A

A

A

P

A

A

S

C

K

K

M

V

A

D

A

N

T

V

R

K

E

R

Y

Y

G

G

A

G

Q

H

V

I

T

W

Y

S

N

D

R

V

Y

S

T

I

E

E

D

S

R

R

E

E

A

S

I

V

S

A

R

K

Q

R

L

V

A

Q

H

E

E

E

R

T

G

G

M

A

T

I

L

L

I

V

P

H

P

P

F

F

D

N

H

N

P

K

H

N

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

A

V

A

S

L

L

E

E

L

L

Q

E

E

E

V

V

P

P

D

E

L

I

D

D

Y

T

L

I

F

I

V

V

C

P

L

I

G

S

G

G

L

L

L

I

S

S

G

G

S

V

L

A

L

L

A

A

Q

K

A

A

L

I

A

N

P

P

R

S

C

I

K

R

V

I

I

L

G

A

V

A

E
|
E

P

P

E

K

T

G

A

A

N

D

D
|
D

A

S

Q

A

Q

Q

S

S

L

K

R

A

A

A

G

G

H

K

I

I

V

I

R

T

I

L

P

P

N

S

P

T

H

N

T

T

I

I

A

A

D

D

G

G

A

L

Q

R

A

A

P

-

S

F

L

L

G

G

E

D

L

L

T

T

Y

W

P

P

I

V

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

I

T

V

V

V

S

D

D

D

Q

N

Q

A

L

I

I

V

Q

D

A

A

L

M

R

K

F

M

F

C

A

Y

E

E

R

M

M

L

K

K

V

V

V

A

V

V

E

E

P

P

T

S

G

G

A

A

L

I

A

G

F

L

A

A

G

A

V

-

Q

-

A

A

F

L

S

S

G

D

E

E

-

F

D

K

D

Q

G

S

A

S

K

A

L

W

L

H

Q

E

G

S

E

S

H

K

V

I

G

G

V

I

I

I

V

V

S

S

G

G

N

N

V

V

D

D

L

L

P

G

R

V

L

L

A

W

R

E

F

S

L

L

E219 (= E213) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (= D219) 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)
43% identity, 95% coverage: 16:332/334 of query aligns to 6:320/329 of 5cvcA

query
sites
5cvcA

D

D

D

S

V

I

A

R

A

E

A

A

A

Q

R

A

R

R

L

I

A

A

G

P

V

Y

A

V

H

H

H

R

T

T

P

P

V

V

M

M

R

S

C

S

N

T

T

S

I

I

D

D

E

A

R

M

L

V

G

G

A

K

K

K

L

L

F

F

K

K

C

C

E

E

N

C

L

F

Q

Q

R

K

T

A

G

G

A

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

S

N

N

A

S

L

I

A

F

Q

A

F

L

S

D

D

D

A

E

Q

Q

R

V

E

S

H

K

G

G

V

V

L

V

T

T

F

H

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

A

A

A

I

V

A

A

L

L

S

A

A

A

R

K

L

L

L

R

D

G

M

I

P

P

A

A

L

H

V

I

V

V

M

I

P

P

E

R

D

N

A

A

A

P

A

A

S

S

K

K

M

V

A

E

A

N

T

V

R

K

E

C

Y

Y

G

G

A

G

Q

H

V

I

T

W

Y

S

N

D

R

A

Y

S

T

I

E

E

D

S

R

R

E

E

A

Y

I

V

S

S

R

K

Q

R

L

V

A

Q

H

E

E

E

R

T

G

G

M

A

T

V

L

L

I

I

P

H

P

P

F

I

D

N

H

S

P

K

H

Y

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

A

V

A

S

L

L

E

E

L

L

Q

E

E

Q

V

V

P

P

D

E

L

I

D

D

Y

T

L

I

F

I

V

V

C

P

L

I

G
x
S

G
|
G

L

L

L

I

S

S

G

G

S

V

L

A

L

L

A

A

Q

K

A

A

L

I

A

N

P

P

R

S

C

I

K

R

V

I

I

L

G

A

V

A

E
|
E

P

P

E

K

T

G

A
|
A

N

D

D
|
D

A

S

Q

A

Q

Q

S

S

L

K

R

A

A

A

G

G

H

K

I

I

V

I

R

T

I

L

P

P

N

S

P

T

H

N

T

T

I

I

A

A

D

D

G
|
G

A
x
L

Q

R

A

A

P

-

S

F

L

L

G

G

E

D

L

L

T

T

Y

W

P

P

I

V

R

R

E

D

H

L

V

V

E

D

D

D

I

V

V

I

T

V

V

V

S

D

D

D

Q

T

Q

A

L

I

I

V

Q

D

A

A

L

M

R

K

F

M

F

C

A

Y

E

E

R

I

M

L

K

K

V

V

V

A

V

V

E
|
E

P

P

T

S

G

G

A

A

L

I

A

G

F

L

A

A

G

A

V

-

Q

-

A

A

F

L

S

S

G

D

E

E

-

F

D

K

D

Q

G

S

A

S

K

A

L

W

L

H

Q

E

G

S

E

S

H

K

V

I

G

G

V

I

I

I

V
|
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

L

L

P

G

R

T

L

L

A

W

R

Q

F

S

L

M

active site: K52 (= K62), S77 (≠ A87), E203 (= E213), A207 (= A217), D209 (= D219), G231 (= G241), V306 (= V318), S307 (= S319)
binding magnesium ion: E203 (= E213), A207 (= A217), D209 (= D219)
binding pyridoxal-5'-phosphate: F51 (= F61), K52 (= K62), N79 (= N89), S178 (≠ G188), G179 (= G189), G180 (= G190), G181 (= G191), L232 (≠ A242), E275 (= E286), S307 (= S319), G308 (= G320)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
40% identity, 93% coverage: 17:325/334 of query aligns to 9:312/322 of 3l6bA

query
sites
3l6bA

D

D

V

V

A

E

A

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

V

S

A

I

H

H

H

L

T

T

P

P

V

V

M

L

R

T

C

S

N

S

T

I

I

L

D

N

E

Q

R

L

L

T

G

G

A

R

K

N

L

L

F

F

K

K

C

C

E

E

N

L

L

F

Q

Q

R

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

A

A

L

V

A

R

Q

S

F

L

S

-

D

-

A

V

Q

R

R

K

E

P

H

K

G

A

V

V

L

V

T

T

F

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

A

A

I

L

A

T

L

Y

S

A

A

A

R

K

L

L

L

E

D

G

M

I

P

P

A

A

L

Y

V

I

V

V

M

V

P

P

E

Q

D

T

A

A

A

P

A

D

S

C

K

K

M

K

A

L

A

A

T

I

R

Q

E

A

Y

Y

G

G

A

A

Q

S

V

I

V

V

T

Y

Y

C

N

E

R

P

Y

S

T

D

E

E

D

S

R
|
R

E

E

A

N

I

V

S

A

R

K

Q

R

L

V

A

T

H

E

E

E

R

T

G

E

M

G

T

I

L

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

Q

N

E

Q

V

V

P

P

D

L

L

V

D

D

Y

A

L

L

F

V

V

V

C

P

L

V

G
|
G

L
x
M

L

L

S

A

G

G

S

I

L

A

L

I

A

T

A

V

Q

K

A

A

L

L

A

K

P

P

R

S

C

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

T

N

A
|
A

N

D

D
|
D

A

C

Q

Y

Q

Q

S

S

L

K

R

L

A

K

G

G

H

K

I

L

V

-

R

-

I

M

P

P

N

N

-

L

-

Y

-

P

P

P

H

E

T

T

I

I

A

A

D

D

G
|
G

A
x
V

Q

K

A

S

P

-

S

S

L

I

G

G

E

L

L

N

T

T

Y

W

P

P

I

I

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

F

T

T

V

V

S

T

D

E

Q

D

Q

E

L

I

I

K

Q

C

A

A

L

T

R

Q

F

L

F

V

A

W

E

E

R

R

M

M

K

K

V

L

V

I

E
|
E

P

P

T
|
T

G

A

A

G

L

V

A

G

F

V

A

A

G

A

V

V

-

L

-

S

Q

Q

A

H

F

F

S

Q

G

T

E

V

D

S

D

P

G

E

A

V

K

K

L

-

Q

-

G

-

E

-

H

N

V

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

L

L

active site: K54 (= K62), S77 (≠ A87), E203 (= E213), A207 (= A217), D209 (= D219), G232 (= G241), T278 (= T288), L305 (≠ V318), S306 (= S319)
binding malonate ion: K54 (= K62), S76 (= S86), S77 (≠ A87), N79 (= N89), H80 (= H90), R128 (= R138), G232 (= G241)
binding manganese (ii) ion: E203 (= E213), A207 (= A217), D209 (= D219)
binding pyridoxal-5'-phosphate: F53 (= F61), K54 (= K62), N79 (= N89), G178 (= G188), G179 (= G189), G180 (= G190), G181 (= G191), M182 (≠ L192), V233 (≠ A242), E276 (= E286), T278 (= T288), S306 (= S319), G307 (= G320)

6zspAAA serine racemase bound to atp and malonate. (see paper)
40% identity, 93% coverage: 17:325/334 of query aligns to 8:309/320 of 6zspAAA

query
sites
6zspAAA

D

D

V

V

A

E

A

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

V

S

A

I

H

H

H

L

T

T

P

P

V

V

M

L

R

T

C
x
S

N
x
S

T
x
I

I

L

D

N

E

Q

R

L

L

T

G

G

A

R

K

N

L

L

F

F

K

K

C

C

E

E

N

L

L

F

Q

Q

R
x
K

T
|
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

A

A

L

V

A

R

Q

S

F

L

S

-

D

-

A

-

Q

-

R

K

E

P

H

K

G

A

V

V

L

V

T

T

F

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

A

A

I

L

A

T

L

Y

S

A

A

A

R

K

L

L

L

E

D

G

M

I

P

P

A

A

L

Y

V

I

V

V

M

V

P

P

E

Q

D

T

A

A

A

P

A

D

S

C

K

K

M

K

A

L

A

A

T

I

R

Q

E

A

Y
|
Y

G

G

A

A

Q

S

V

I

V

V

T

Y

Y

C

N

E

R

P

Y

S

T

D

E

E

D

S

R
|
R

E

E

A

N

I

V

S

A

R

K

Q

R

L

V

A

T

H

E

E

E

R

T

G

E

M

G

T

I

L

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

Q

N

E

Q

V

V

P

P

D

L

L

V

D

D

Y

A

L

L

F

V

V

V

C

P

L

V

G

G

L

M

L

L

S

A

G

G

S

I

L

A

L

I

A

T

A

V

Q

K

A

A

L

L

A

K

P

P

R

S

C

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

T

N

A
|
A

N

D

D
|
D

A

C

Q

Y

Q

Q

S

S

L

K

R

L

A

K

G

G

H

K

I

L

V

-

R

-

I

M

P

P

N

N

-

L

-

Y

-

P

P

P

H

E

T

T

I

I

A

A

D

D

G
|
G

A

V

Q

K

A
x
S

P

-

S

S

L

I

G

G

E

L

L

N

T

T

Y

W

P

P

I

I

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

F

T

T

V

V

S

T

D

E

Q

D

Q

E

L

I

I

K

Q

C

A

A

L

T

R

Q

F

L

F

V

A

W

E
|
E

R
|
R

M

M

K
|
K

V

L

V

I

E

E

P

P

T

T

G

A

A

G

L

V

A

G

F

V

A

A

G

A

V

V

-

L

-

S

Q

Q

A

H

F

F

S

Q

G

T

E

V

D

S

D

P

G

E

A

V

K

K

L

-

Q

-

G

-

E

-

H

N

V

I

G

C

V

I

I

V

V
x
L

S
|
S

G

G

N
|
N

V

V

D

D

L

L

active site: K53 (= K62), S74 (≠ A87), E200 (= E213), A204 (= A217), D206 (= D219), G229 (= G241), L302 (≠ V318), S303 (= S319)
binding adenosine-5'-triphosphate: S28 (≠ C37), S29 (≠ N38), I30 (≠ T39), K48 (≠ R57), T49 (= T58), Q79 (= Q92), Y111 (= Y124), E266 (= E279), R267 (= R280), K269 (= K282), N306 (= N322)
binding magnesium ion: E200 (= E213), A204 (= A217), D206 (= D219)
binding malonate ion: K53 (= K62), S73 (= S86), S74 (≠ A87), N76 (= N89), H77 (= H90), R125 (= R138), G229 (= G241), S232 (≠ A244)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
40% identity, 93% coverage: 17:325/334 of query aligns to 8:316/322 of 7nbgAAA

query
sites
7nbgAAA

D

D

V

V

A

E

A

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

V

S

A

I

H

H

H

L

T

T

P

P

V

V

M

L

R

T

C

S

N

S

T

I

I

L

D

N

E

Q

R

L

L

T

G

G

A

R

K

N

L

L

F

F

K

K

C

C

E

E

N

L

L

F

Q

Q

R

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

A

A

L

V

A

R

Q

S

F

L

-

V

S

P

D

D

A

A

-

L

-

E

Q

R

R

K

E

P

H

K

G

A

V

V

L

V

T

T

F

H

S

S

A
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

A

A

I

L

A

T

L

Y

S

A

A

A

R

K

L

L

L

E

D

G

M

I

P

P

A

A

L

Y

V
x
I

V

V

M

V

P

P

E

Q

D

T

A

A

A

P

A

D

S

C

K
|
K

M

K

A

L

A

A

T
x
I

R

Q

E

A

Y
|
Y

G

G

A

A

Q

S

V

I

V

V

T

Y

Y

C

N

E

R

P

Y

S

T

D

E

E

D

S

R

R

E

E

A

N

I

V

S

A

R

K

Q

R

L

V

A

T

H

E

E

E

R

T

G

E

M

G

T

I

L

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

Q

N

E

Q

V

V

P

P

D

L

L

V

D

D

Y

A

L

L

F

V

V

V

C

P

L

V

G
|
G

L
x
M

L

L

S

A

G

G

S

I

L

A

L

I

A

T

A

V

Q

K

A

A

L

L

A

K

P

P

R

S

C

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

T

N

A
|
A

N

D

D
|
D

A

C

Q

Y

Q

Q

S

S

L

K

R

L

A

K

G

G

H

K

I

L

V

-

R

-

I

M

P

P

N

N

-

L

-

Y

-

P

P

P

H

E

T

T

I

I

A

A

D

D

G
|
G

A
x
V

Q

K

A

S

P

-

S

S

L

I

G

G

E

L

L

N

T

T

Y

W

P

P

I

I

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

F

T

T

V

V

S

T

D

E

Q

D

Q

E

L

I

I

K

Q

C

A

A

L

T

R

Q

F

L

F

V

A

W

E

E

R

R

M

M

K

K

V

L

V

I

E

E

P

P

T
|
T

G

A

A

G

L

V

A

G

F

V

A

A

G

A

V

V

-

L

-

S

Q

Q

A

H

F

F

S

Q

G

T

E

V

D

S

D

P

G

E

A

V

K

K

L

-

Q

-

G

-

E

-

H

N

V

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

L

L

active site: K53 (= K62), S81 (≠ A87), E207 (= E213), A211 (= A217), D213 (= D219), G236 (= G241), L309 (≠ V318), S310 (= S319)
binding calcium ion: E207 (= E213), A211 (= A217), D213 (= D219)
binding pyridoxal-5'-phosphate: F52 (= F61), K53 (= K62), N83 (= N89), G182 (= G188), G183 (= G189), G184 (= G190), G185 (= G191), M186 (≠ L192), G236 (= G241), V237 (≠ A242), T282 (= T288), S310 (= S319), G311 (= G320)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A87), G85 (≠ A91), Q86 (= Q92), I101 (≠ V107), K111 (= K117), I115 (≠ T121), Y118 (= Y124)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
40% identity, 93% coverage: 17:325/334 of query aligns to 8:316/323 of 7nbfAAA

query
sites
7nbfAAA

D

D

V

V

A

E

A

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

V

S

A

I

H
|
H

H
x
L

T
|
T

P
|
P

V

V

M
x
L

R
x
T

C

S

N

S

T

I

I

L

D

N

E

Q

R

L

L

T

G

G

A

R

K

N

L

L

F

F

K

K

C

C

E

E

N

L

L
x
F

Q

Q

R

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

A

A

L

V

A

R

Q

S

F

L

-

V

S

P

D

D

A

A

-

L

-

E

Q

R

R

K

E

P

H

K

G

A

V

V

L

V

T

T

F

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

A

A

I

L

A

T

L

Y

S

A

A

A

R

K

L

L

L

E

D

G

M

I

P

P

A

A

L

Y

V

I

V

V

M

V

P

P

E

Q

D

T

A

A

A

P

A

D

S

C

K

K

M

K

A

L

A

A

T

I

R

Q

E

A

Y

Y

G

G

A

A

Q

S

V

I

V

V

T

Y

Y

C

N

E

R

P

Y

S

T

D

E

E

D

S

R

R

E

E

A

N

I

V

S

A

R

K

Q

R

L

V

A

T

H

E

E

E

R

T

G

E

M

G

T

I

L

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

Q

N

E

Q

V

V

P

P

D

L

L

V

D

D

Y

A

L

L

F

V

V

V

C

P

L

V

G
|
G

L
x
M

L

L

S

A

G

G

S

I

L

A

L

I

A

T

A

V

Q

K

A

A

L

L

A

K

P

P

R

S

C

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

T

N

A
|
A

N

D

D
|
D

A

C

Q

Y

Q

Q

S

S

L

K

R

L

A

K

G

G

H

K

I

L

V

-

R

-

I

M

P

P

N

N

-

L

-

Y

-

P

P

P

H

E

T

T

I

I

A

A

D

D

G
|
G

A
x
V

Q

K

A

S

P

-

S

S

L

I

G

G

E

L

L
x
N

T

T

Y

W

P

P

I

I

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

F

T

T

V

V

S

T

D

E

Q

D

Q

E

L

I

I

K

Q

C

A

A

L

T

R

Q

F

L

F

V

A

W

E

E

R

R

M

M

K

K

V

L

V

I

E

E

P

P

T
|
T

G

A

A

G

L

V

A

G

F

V

A

A

G

A

V

V

-

L

-

S

Q

Q

A

H

F

F

S

Q

G

T

E

V

D

S

D

P

G

E

A

V

K

K

L

-

Q

-

G

-

E

-

H

N

V

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

L

L

active site: K53 (= K62), S81 (≠ A87), E207 (= E213), A211 (= A217), D213 (= D219), G236 (= G241), L309 (≠ V318), S310 (= S319)
binding calcium ion: E207 (= E213), A211 (= A217), D213 (= D219)
binding magnesium ion: N244 (≠ L250)
binding pyridoxal-5'-phosphate: F52 (= F61), K53 (= K62), N83 (= N89), G182 (= G188), G183 (= G189), G184 (= G190), G185 (= G191), M186 (≠ L192), G236 (= G241), V237 (≠ A242), T282 (= T288), S310 (= S319), G311 (= G320)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (= H30), L22 (≠ H31), T23 (= T32), P24 (= P33), L26 (≠ M35), T27 (≠ R36), F46 (≠ L55)

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)
40% identity, 93% coverage: 17:325/334 of query aligns to 8:316/323 of 7nbdAAA

query
sites
7nbdAAA

D

D

V

V

A

E

A

K

A

A

A

H

R

I

R

N

L

I

A

R

G

D

V

S

A

I

H

H

H

L

T

T

P

P

V

V

M

L

R

T

C

S

N

S

T

I

I

L

D

N

E

Q

R

L

L

T

G

G

A

R

K

N

L

L

F

F

K

K

C

C

E

E

N

L

L

F

Q

Q

R

K

T

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

A

A

L

V

A

R

Q

S

F

L

-

V

S

P

D

D

A

A

-

L

-

E

Q

R

R

K

E

P

H

K

G

A

V

V

L

V

T

T

F

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

A

A

I

L

A

T

L

Y

S

A

A

A

R

K

L

L

L

E

D

G

M

I

P

P

A

A

L

Y

V

I

V

V

M

V

P

P

E

Q

D

T

A

A

A

P

A

D

S

C

K

K

M

K

A

L

A

A

T

I

R

Q

E

A

Y

Y

G

G

A

A

Q

S

V

I

V

V

T

Y

Y

C

N

E

R

P

Y

S

T

D

E

E

D

S

R

R

E

E

A

N

I

V

S

A

R

K

Q

R

L

V

A

T

H

E

E

E

R

T

G

E

M

G

T

I

L

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

Q

N

E

Q

V

V

P

P

D

L

L

V

D

D

Y

A

L

L

F

V

V

V

C

P

L

V

G
|
G

L
x
M

L

L

S

A

G

G

S

I

L

A

L

I

A

T

A

V

Q

K

A

A

L

L

A

K

P

P

R

S

C

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

T

N

A
|
A

N

D

D
|
D

A

C

Q

Y

Q

Q

S

S

L

K

R

L

A

K

G

G

H

K

I

L

V

-

R

-

I

M

P

P

N

N

-

L

-

Y

-

P

P

P

H

E

T

T

I

I

A

A

D

D

G
|
G

A
x
V

Q

K

A

S

P

-

S

S

L

I

G

G

E

L

L
x
N

T

T

Y

W

P

P

I

I

R

R

E

D

H

L

V

V

E

D

D

D

I

I

V

F

T

T

V

V

S

T

D

E

Q

D

Q

E

L

I

I

K

Q

C

A

A

L

T

R

Q

F

L

F

V

A
x
W

E

E

R

R

M

M

K

K

V

L

V
x
L

V

I

E
|
E

P

P

T
|
T

G

A

A

G

L

V

A

G

F

V

A

A

G

A

V

V

-

L

-

S

Q

Q

A

H

F

F

S

Q

G

T

E

V

D

S

D

P

G

E

A

V

K

K

L

-

Q

-

G

-

E

-

H

N

V

I

G

C

V

I

I

V

V
x
L

S
|
S

G
|
G

G

G

N

N

V
|
V

D

D

L
|
L

active site: K53 (= K62), S81 (≠ A87), E207 (= E213), A211 (= A217), D213 (= D219), G236 (= G241), L309 (≠ V318), S310 (= S319)
binding calcium ion: E207 (= E213), A211 (= A217), D213 (= D219)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ A278), L278 (≠ V284), V314 (= V323), L316 (= L325)
binding magnesium ion: N244 (≠ L250)
binding pyridoxal-5'-phosphate: F52 (= F61), K53 (= K62), N83 (= N89), G182 (= G188), G183 (= G189), G184 (= G190), G185 (= G191), M186 (≠ L192), G236 (= G241), V237 (≠ A242), E280 (= E286), T282 (= T288), S310 (= S319), G311 (= G320)

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)
40% identity, 93% coverage: 17:325/334 of query aligns to 8:316/323 of 7nbcCCC

query
sites
7nbcCCC

D

D

V

V

A

E

A

K

A

A