SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing GFF3797 FitnessBrowser__psRCH2:GFF3797 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)

P04968 L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 from Escherichia coli (strain K12) (see paper)
53% identity, 99% coverage: 5:503/504 of query aligns to 16:512/514 of P04968

query
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P04968

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K62 (= K51) modified: N6-(pyridoxal phosphate)lysine
N89 (= N78) binding
GGGGL 188:192 (= GGGGL 178:182) binding
S315 (= S305) binding

1tdjA Threonine deaminase (biosynthetic) from e. Coli (see paper)
52% identity, 99% coverage: 5:503/504 of query aligns to 12:492/494 of 1tdjA

query
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1tdjA

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active site: K58 (= K51), A83 (= A76), E209 (= E203), S213 (= S207), C215 (= C209), G237 (= G231), L310 (≠ D304), S311 (= S305)
binding pyridoxal-5'-phosphate: F57 (= F50), K58 (= K51), N85 (= N78), G184 (= G178), G185 (= G179), G186 (= G180), G187 (= G181), G237 (= G231), E282 (= E276), S311 (= S305), G312 (= G306)

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
40% identity, 62% coverage: 7:318/504 of query aligns to 16:322/326 of 2gn2A

query
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2gn2A

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A

I

L

Y

I

D

Q

D

R

T

N

R

K

S

V

I

I

T

T

E

E

P

G

A

A

G

G

A

A

L

L

S

A

V

C

A

A

G

A

I

L

K

L

K

S

Y

G

V

K

E

L

R

D

E

S

G

H

V

I

S

Q

G

N

Q

R

V

K

L

T

V

V

G

S

I

I

D
x
I

S
|
S

G

G

A

G

N
|
N

V

I

N

D

F

L

D

S

R

R

L

V

R

S

H

Q

V

I

A

T

active site: K56 (= K51), A81 (= A76), Q207 (≠ E203), V211 (≠ S207), G213 (≠ C209), G235 (= G231), I308 (≠ D304), S309 (= S305)
binding cytidine-5'-monophosphate: R51 (≠ P46), T52 (≠ V47), G53 (≠ F48), A114 (≠ G109), D117 (≠ A112), Y118 (≠ R113), N312 (= N308)

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)
37% identity, 60% coverage: 13:313/504 of query aligns to 15:312/319 of A4F2N8

query
sites
A4F2N8

R

R

V

L

Y

E

D

G

V

F

A

A

I

N

E

R

T

T

P

P

L

V

Q

F

P

T

A

S

R

R

Q

T

L

L

S

D

E

A

R

E

I

T

G

G

N

A

Q

Q

I

V

L

F

L

I

K

K

R

C

E

E

D

N

L

L

Q

Q

P

R

V

T

F

G

S

S

F

F

K
|
K

V

F

R

R

G

G

A

A

Y

F

N

N

K

A

L

L

A

S

Q

R

L

F

S

D

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

V

T

A

A

F

S

S

A

S

G

G

N

N

H

H

A

A

Q

Q

G

G

V

I

A

A

L

L

A

A

A

A

K

R

Q

L

L

L

G

Q

I

M

K

P

A

A

T

T

I

I

V

V

M

M

P

P

R

T

T

D

T

A

P

P

E

A

L

A

K

K

V

V

Q

A

G

A

V

T

R

R

A

E

R

Y

G

G

G

A

K

T

V

V

V

V

L

F

H

Y

G

D

D

R

A

I

F

T

P

E

E

D

A

R

L

E

A

Q

Y

I

S

G

L

R

K

T

L

L

V

A

E

E

E

Q

K

H

G

G

Y

M

V

T

Y

L

I

I

H

P

P

S

Y

Y

D

D

D

H

P

P

D

D

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

L

R

-

Q

E

H

F

Q

T

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

G

V

L

G

G

G

G

G

G

G

G

L

M

V

L

A

S

G

G

I

T

A

A

A

L

Y

A

V

T

K

R

Y

A

L

L

Y

S

P

P

Q

D

T

C

K

L

V

L

I

Y

G

G

V

V

E

E

P

P

D

E

D

A

S

G

N

N

C

D

L

G

Q

Q

A

R

A

S

M

F

A

Q

A

T

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

A

L

T

F

I

A

A

D

D

G

G

V

A

A

Q

V

T

A

Q

Q

H

I

L

G

G

Q

N

H

H

T

T

F

F

E

P

I

I

C

I

R

R

H

E

Y

N

V

V

D

N

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

A

E

E

I

L

C

V

A

E

A

S

I

M

K

R

D

F

I

F

Y

M

D

Q

D

R

T

M

R

K

S

M

I

V

T

V

E

E

P

P

A

T

G

G

A

C

L

L

S

G

V

L

A

A

G

A

I

L

K

R

K

N

Y

L

V

-

E

-

R

K

E

Q

G

Q

V

F

S

R

G

G

Q

Q

V

R

L

V

V

G

G

I

I

I

D

V

S

T

G

G

A

G

N

N

V

V

N

D

F

I

D

E

R

K

K53 (= K51) mutation to A: Loss of enzymatic activity.

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)
36% identity, 61% coverage: 11:316/504 of query aligns to 17:319/323 of O59791

query
sites
O59791

T

S

S

E

R

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

T

L

V

S

N

E

K

R

E

I

F

G

V

N

A

Q

E

I

V

L

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F

F

K

K

V

F

R

R

G

G

A

A

Y

L

N

N

K

A

L

L

A

S

Q

Q

L

L

S

N

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

L

T

T

A

F

S

S

A
x
S

G

G

N

N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

K

K

Q

I

L

L

G

G

I

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

E

E

L

A

K

K

V

V

Q

A

G

A

V

T

R

K

A

G

R

Y

G

G

G

G

K

Q

V

V

V

I

L

M

H

Y

G

D

D

R

A

Y

F

K

P

D

E

D

A

R

L

E

A

K

Y

M

S

A

L

K

K

E

L

I

V

S

E

E

E

R

K

E

G

G

Y

L

V

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

F

R

-

Q

E

H

E

Q

V

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

C

V

L

G

G

G

G

G

G

G

G

L

L

V

L

A

S

G

G

I

S

A

A

A

L

Y

A

V

A

K

R

Y

H

L

F

Y

A

P

P

Q

N

T

C

K

E

V

V

I

Y

G

G

V

V

E

E

P

P

D

E

D

A

S

G

N

N

C

D

L

G

Q

Q

A

Q

A

S

M

F

A

R

A

K

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G

G

V

A

A

Q

V

T

A

Q

Q

H

I

L

G

G

Q

N

H

Y

T

T

F

F

E

S

I

I

C

I

R

K

H

E

Y

K

V

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

I

L

K

K

D

F

I

Y

Y

A

D

A

D

R

T

M

R

K

S

I

I

V

T

V

E

E

P

P

A

T

G

G

A

C

L

L

S

S

V

F

A

A

G

A

I

A

K

R

K

A

Y

M

V

-

E

-

R

K

E

E

G

K

V

L

S

K

G

N

Q

K

V

R

L

I

V

G

G

I

I

I

D

I

S

S

G

G

A

G

N

N

V

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

S82 (≠ A76) 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)
36% identity, 61% coverage: 11:316/504 of query aligns to 13:315/319 of 2zr8A

query
sites
2zr8A

T

S

S

E

R

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

T

L

V

S

N

E

K

R

E

I

F

G

V

N

A

Q

E

I

V

L

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

V

F

R

R

G

G

A

A

Y

L

N

N

K

A

L

L

A

S

Q

Q

L

L

S

N

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

L

T

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

K

K

Q

I

L

L

G

G

I

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

E

E

L

A

K

K

V

V

Q

A

G

A

V

T

R

K

A

G

R

Y

G

G

G

G

K

Q

V

V

V

I

L

M

H

Y

G

D

D

R

A

Y

F

K

P

D

E

D

A
x
R

L

E

A

K

Y

M

S

A

L

K

K

E

L

I

V

S

E

E

E

R

K

E

G

G

Y

L

V

T

Y

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

F

R

-

Q

E

H

E

Q

V

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

C

V

L

G
|
G

G
|
G

G
|
G

G
|
G

L

L

V

L

A

S

G

G

I

S

A

A

A

L

Y

A

V

A

K

R

Y

H

L

F

Y

A

P

P

Q

N

T

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

D

E

D

A

S
x
G

N

N

C
x
D

L

G

Q

Q

A

Q

A

S

M

F

A

R

A

K

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

K

L

T

F

I

A

A

D
|
D

G
|
G

V
x
A

A
x
Q

V
x
T

A

Q

Q

H

I

L

G

G

Q

N

H

Y

T

T

F

F

E

S

I

I

C

I

R

K

H

E

Y

K

V

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

I

L

K

K

D

F

I

Y

Y

A

D

A

D

R

T

M

R

K

S

I

I

V

T

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

S

S

V

F

A

A

G

A

I

A

K

R

K

A

Y

M

V

-

E

-

R

K

E

E

G

K

V

L

S

K

G

N

Q

K

V

R

L

I

V

G

G

I

I

I

D
x
I

S
|
S

G

G

A

G

N

N

V

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

active site: K53 (= K51), S78 (≠ A76), E204 (= E203), G208 (≠ S207), D210 (≠ C209), G232 (= G231), I303 (≠ D304), S304 (= S305)
binding magnesium ion: E204 (= E203), G208 (≠ S207), D210 (≠ C209)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F50), K53 (= K51), S77 (= S75), S78 (≠ A76), N80 (= N78), H81 (= H79), P147 (= P145), G179 (= G178), G180 (= G179), G181 (= G180), G182 (= G181), G232 (= G231), E277 (= E276), T279 (≠ A278), S304 (= S305)
binding serine: S78 (≠ A76), R129 (≠ A127), D231 (= D230), G232 (= G231), A233 (≠ V232), Q234 (≠ A233), T235 (≠ V234)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
36% identity, 61% coverage: 11:316/504 of query aligns to 13:315/319 of 2zpuA

query
sites
2zpuA

T

S

S

E

R

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

T

L

V

S

N

E

K

R

E

I

F

G

V

N

A

Q

E

I

V

L

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

V

F

R

R

G

G

A

A

Y

L

N

N

K

A

L

L

A

S

Q

Q

L

L

S

N

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

L

T

T

A

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

K

K

Q

I

L

L

G

G

I

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

E

E

L

A

K

K

V

V

Q

A

G

A

V

T

R

K

A

G

R

Y

G

G

G

G

K

Q

V

V

V

I

L

M

H

Y

G

D

D

R

A

Y

F

K

P

D

E

D

A

R

L

E

A

K

Y

M

S

A

L

K

K

E

L

I

V

S

E

E

E

R

K

E

G

G

Y

L

V

T

Y

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

F

R

-

Q

E

H

E

Q

V

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

C

V

L

G
|
G

G
|
G

G
|
G

G
|
G

L

L

V

L

A

S

G

G

I

S

A

A

A

L

Y

A

V

A

K

R

Y

H

L

F

Y

A

P

P

Q

N

T

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

D

E

D

A

S
x
G

N

N

C
x
D

L

G

Q

Q

A

Q

A

S

M

F

A

R

A

K

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

I

L

G

G

Q

N

H

Y

T

T

F

F

E

S

I

I

C

I

R

K

H

E

Y

K

V

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

I

L

K

K

D

F

I

Y

Y

A

D

A

D

R

T

M

R

K

S

I

I

V

T

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

S

S

V

F

A

A

G

A

I

A

K

R

K

A

Y

M

V

-

E

-

R

K

E

E

G

K

V

L

S

K

G

N

Q

K

V

R

L

I

V

G

G

I

I

I

D
x
I

S
|
S

G

G

A

G

N

N

V

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

active site: K53 (= K51), S78 (≠ A76), E204 (= E203), G208 (≠ S207), D210 (≠ C209), G232 (= G231), I303 (≠ D304), S304 (= S305)
binding magnesium ion: E204 (= E203), G208 (≠ S207), D210 (≠ C209)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F50), K53 (= K51), S77 (= S75), S78 (≠ A76), N80 (= N78), H81 (= H79), P147 (= P145), G179 (= G178), G180 (= G179), G181 (= G180), G182 (= G181), G232 (= G231), E277 (= E276), T279 (≠ A278), S304 (= S305)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
36% identity, 61% coverage: 11:316/504 of query aligns to 12:314/318 of 1wtcA

query
sites
1wtcA

T

S

S

E

R

R

V

I

Y

K

D

K

V

F

A

A

I
x
N

E

K

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

T

L

V

S

N

E

K

R

E

I

F

G

V

N

A

Q

E

I

V

L

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P
x
K

V
x
M

F

G

S

A

F
|
F

K
|
K

V

F

R

R

G

G

A

A

Y

L

N

N

K

A

L

L

A

S

Q

Q

L

L

S

N

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

L

T

T

A

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

K

K

Q

I

L

L

G

G

I

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

E

E

L

A

K

K

V

V

Q
x
A

G
x
A

V

T

R

K

A

G

R
x
Y

G

G

G

G

K

Q

V

V

V

I

L

M

H

Y

G

D

D

R

A

Y

F

K

P

D

E

D

A

R

L

E

A

K

Y

M

S

A

L

K

K

E

L

I

V

S

E

E

E

R

K

E

G

G

Y

L

V

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

F

R

-

Q

E

H

E

Q

V

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

C

V

L

G
|
G

G
|
G

G
|
G

G
|
G

L

L

V

L

A

S

G

G

I

S

A

A

A

L

Y

A

V

A

K

R

Y

H

L

F

Y

A

P

P

Q

N

T

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

D

E

D

A

S
x
G

N

N

C
x
D

L

G

Q

Q

A

Q

A

S

M

F

A

R

A

K

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

I

L

G

G

Q

N

H

Y

T

T

F

F

E

S

I

I

C

I

R

K

H

E

Y

K

V

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

I

L

K

K

D

F

I

Y

Y

A

D

A

D

R

T

M

R

K

S

I

I

V

T

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

S

S

V

F

A

A

G

A

I

A

K

R

K

A

Y

M

V

-

E

-

R

K

E

E

G

K

V

L

S

K

G

N

Q

K

V

R

L

I

V

G

G

I

I

I

D
x
I

S
|
S

G

G

A

G

N

N

V

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

active site: K52 (= K51), S77 (≠ A76), E203 (= E203), G207 (≠ S207), D209 (≠ C209), G231 (= G231), I302 (≠ D304), S303 (= S305)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ I19), K47 (≠ P46), M48 (≠ V47), A109 (≠ Q108), A110 (≠ G109), Y114 (≠ R113)
binding magnesium ion: E203 (= E203), G207 (≠ S207), D209 (≠ C209)
binding pyridoxal-5'-phosphate: F51 (= F50), K52 (= K51), N79 (= N78), G178 (= G178), G179 (= G179), G180 (= G180), G181 (= G181), G231 (= G231), E276 (= E276), T278 (≠ A278), S303 (= S305)

1v71A Crystal structure of s.Pombe serine racemase
36% identity, 61% coverage: 11:316/504 of query aligns to 12:314/318 of 1v71A

query
sites
1v71A

T

S

S

E

R

R

V

I

Y

K

D

K

V

F

A

A

I

N

E

K

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

T

L

V

S

N

E

K

R

E

I

F

G

V

N

A

Q

E

I

V

L

F

L

F

K

K

R

C

E

E

D

N

L

F

Q

Q

P

K

V

M

F

G

S

A

F
|
F

K
|
K

V

F

R

R

G

G

A

A

Y

L

N

N

K

A

L

L

A

S

Q

Q

L

L

S

N

A

E

E

A

E

Q

L

R

A

K

R

A

G

G

V

V

V

L

T

T

A

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

K

K

Q

I

L

L

G

G

I

I

K

P

A

A

T

K

I

I

V

I

M

M

P

P

R

L

T

D

T

A

P

P

E

E

L

A

K

K

V

V

Q

A

G

A

V

T

R

K

A

G

R

Y

G

G

G

G

K

Q

V

V

V

I

L

M

H

Y

G

D

D

R

A

Y

F

K

P

D

E

D

A

R

L

E

A

K

Y

M

S

A

L

K

K

E

L

I

V

S

E

E

E

R

K

E

G

G

Y

L

V

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

P

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

M

K

E

E

I

L

L

F

R

-

Q

E

H

E

Q

V

G

G

P

P

I

L

D

D

A

A

I

L

F

F

V

V

P

C

V

L

G
|
G

G
|
G

G
|
G

G
|
G

L

L

V

L

A

S

G

G

I

S

A

A

A

L

Y

A

V

A

K

R

Y

H

L

F

Y

A

P

P

Q

N

T

C

K

E

V

V

I

Y

G

G

V

V

E
|
E

P

P

D

E

D

A

S
x
G

N

N

C
x
D

L

G

Q

Q

A

Q

A

S

M

F

A

R

A

K

G

G

E

S

R

I

V

V

V

H

L

I

E

D

Q

T

V

P

G

K

L

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

I

L

G

G

Q

N

H

Y

T

T

F

F

E

S

I

I

C

I

R

K

H

E

Y

K

V

V

D

D

E

D

V

I

I

L

T

T

V

V

S

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

I

L

K

K

D

F

I

Y

Y

A

D

A

D

R

T

M

R

K

S

I

I

V

T

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

S

S

V

F

A

A

G

A

I

A

K

R

K

A

Y

M

V

-

E

-

R

K

E

E

G

K

V

L

S

K

G

N

Q

K

V

R

L

I

V

G

G

I

I

I

D
x
I

S
|
S

G
|
G

A

G

N

N

V

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

active site: K52 (= K51), S77 (≠ A76), E203 (= E203), G207 (≠ S207), D209 (≠ C209), G231 (= G231), I302 (≠ D304), S303 (= S305)
binding magnesium ion: E203 (= E203), G207 (≠ S207), D209 (≠ C209)
binding pyridoxal-5'-phosphate: F51 (= F50), K52 (= K51), N79 (= N78), G178 (= G178), G179 (= G179), G180 (= G180), G181 (= G181), G231 (= G231), E276 (= E276), T278 (≠ A278), S303 (= S305), G304 (= G306)

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)
36% identity, 53% coverage: 20:284/504 of query aligns to 37:299/339 of Q7XSN8

query
sites
Q7XSN8

E

K

T

T

P

P

L

V

Q

L

P

S

A

S

R

T

Q

S

L

I

S

D

E

A

R

I

I

V

G

G

N

K

Q

Q

I

L

L

F

L

F

K

K

R

C

E

E

D

C

L

F

Q

Q

P

K

V

A

F

G

S

A

F

F

K

K

V

I

R

R

G

G

A

A

Y

S

N

N

K

S

L

I

A

F

Q

A

L

L

S

D

A

D

E

D

E

E

L

A

A

S

R

K

G

G

V

V

V

V

T

T

A

H

S

S

A

S

G

G

N

N

H

H

A

A

Q

A

G

A

V

V

A

A

L

L

A

A

A

A

K

K

Q

L

L

R

G

G

I

I

K

P

A

A

T

Y

I

I

V

V

M

I

P

P

R

R

T

N

T

A

P

P

E

A

L

C

K

K

V

V

Q

D

G

N

V

V

R

K

A

R

R

Y

G

G

G

G

K

H

V

I

V

I

L

W

H

S

G

D

D

V

A

S

F

I

P

E

E

S

A

R

L

E

A

S

Y

V

S

A

L

K

K

R

L

V

V

Q

E

E

E

E

K

T

G

G

Y

A

V

I

Y

L

I

V

H

H

P

P

Y

F

D

N

D

N

P

K

D

N

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

V

V

A

S

M

L

E

E

I

L

L

L

R

E

Q

E

H

V

Q

P

G

-

P

E

I

I

D

D

A

T

I

I

F

I

V

V

P

P

V

I

G

S

G

G

G

G

G

G

L

L

V

I

A

S

G

G

I

V

A

A

A

L

Y

A

V

A

K

K

Y

A

L

I

Y

N

P

P

Q

S

T

I

K

R

V

I

I

L

G

A

V

A

E
|
E

P

P

D

K

D

G

S

A

N

D

C
x
D

L

S

Q

A

A

Q

A

S

M

K

A

A

A

A

G

G

E

K

R

I

V

I

V

T

L

L

E

P

Q

S

V

T

G

N

L

T

F

I

A

A

D

D

G

G

V

L

A

R

V

-

A

A

Q

F

I

L

G

G

Q

D

H

L

T

T

F

W

E

P

I

V

C

V

R

R

H

D

Y

L

V

V

D

D

E

D

V

I

I

I

T

V

V

V

S

D

T

D

D

N

E

A

I

I

C

V

A

D

A

A

I

M

K

K

D

M

I

C

Y

Y

D

E

D

M

T

L

R

K

S

V

I

A

T

V

E

E

P

P

A

S

G

G

A

A

L

I

S

G

V

L

A

A

E219 (= E203) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ C209) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
37% identity, 53% coverage: 21:286/504 of query aligns to 23:290/320 of 7nbhAAA

query
sites
7nbhAAA

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

I

L

L

S

N

E

Q

R

L

I

T

G

G

N

R

Q

N

I

L

L

F

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F

F

K
|
K

V

I

R

R

G

G

A

A

Y

L

N

N

K

A

L

V

A

R

Q

S

L

L

S

V

A

P

E

D

E

A

L

L

A

E

R

R

-

K

-

P

-

K

G

A

V

V

V

V

T

T

A

H

S

S

A
x
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

A

A

K

K

Q

L

L

E

G

G

I

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

E

D

L

C

K
|
K

V

K

Q

L

G

A

V
x
I

R

Q

A

A

R
x
Y

G

G

G

A

K

S

V

I

V

V

L

Y

H

C

G

E

D

P

A

S

F

D

P

E

E

S

A

R

L

E

A

N

Y

V

S

A

L

K

K

R

L

V

V

T

E

E

E

E

K

T

G

E

Y

G

V

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

D

D

A

A

I

L

F

V

V

V

P

P

V

V

G

G

G

G

G

G

G

G

L

M

V

L

A

A

G

G

I

I

A

A

A

I

Y

T

V

V

K

K

Y

A

L

L

Y

K

P

P

Q

S

T

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

D

S

D

N

S
x
A

-

D

N
x
D

C

C

L

Y

Q

Q

A

S

A

K

M

L

A

K

A

G

G

K

E

L

R

M

V

P

V

N

L

L

E

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D
|
D

G
|
G

V

V

A

K

V

-

A

S

Q

S

I

I

G

G

Q

L

H

N

T

T

F

W

E

P

I

I

C

I

R

R

H

D

Y

L

V

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

I

T

K

Q

D

L

I

V

Y

W

D

E

D

R

T

M

R

K

S

L

I

L

T

I

E

E

P
|
P

A

T

G

A

A

G

L

V

S

G

V

V

A

A

G

A

I

V

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (≠ S207), D213 (≠ N208), G236 (= G231)
binding calcium ion: E207 (= E203), A211 (≠ S207), D213 (≠ N208)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A76), G85 (≠ A80), Q86 (= Q81), K111 (= K106), I115 (≠ V110), Y118 (≠ R113), D235 (= D230), P281 (= P277)

Sites not aligning to the query:

active site: 309, 310
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: 313, 314, 315

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
36% identity, 58% coverage: 21:311/504 of query aligns to 23:316/322 of 7nbgAAA

query
sites
7nbgAAA

T

T

P

P

L

V

Q

L

P

T

A

S

R

S

Q

I

L

L

S

N

E

Q

R

L

I

T

G

G

N

R

Q

N

I

L

L

F

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

Y

L

N

N

K

A

L

V

A

R

Q

S

L

L

S

V

A

P

E

D

E

A

L

L

A

E

R

R

-

K

-

P

-

K

G

A

V

V

V

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

A

A

K

K

Q

L

L

E

G

G

I

I

K

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

E

D

L

C

K
|
K

V

K

Q

L

G

A

V
x
I

R

Q

A

A

R
x
Y

G

G

G

A

K

S

V

I

V

V

L

Y

H

C

G

E

D

P

A

S

F

D

P

E

E

S

A

R

L

E

A

N

Y

V

S

A

L

K

K

R

L

V

V

T

E

E

E

E

K

T

G

E

Y

G

V

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

D

D

A

A

I

L

F

V

V

V

P

P

V

V

G
|
G

G
|
G

G
|
G

G
|
G

L
x
M

V

L

A

A

G

G

I

I

A

A

A

I

Y

T

V

V

K

K

Y

A

L

L

Y

K

P

P

Q

S

T

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

D

S

D

N

S
x
A

-

D

N
x
D

C

C

L

Y

Q

Q

A

S

A

K

M

L

A

K

A

G

G

K

E

L

R

M

V

P

V

N

L

L

E

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

I

I

G

G

Q

L

H

N

T

T

F

W

E

P

I

I

C

I

R

R

H

D

Y

L

V

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

I

T

K

Q

D

L

I

V

Y

W

D

E

D

R

T

M

R

K

S

L

I

L

T

I

E

E

P

P

A
x
T

G

A

A

G

L

V

S

G

V

V

A

A

G

A

I

V

K

L

K

S

Y

Q

V

-

E

H

R

F

E

Q

G

T

V

V

S

S

G

P

Q

E

V

V

-

K

-

N

L

I

V

C

G

I

I

V

D
x
L

S
|
S

G
|
G

A

G

N

N

V

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (≠ S207), D213 (≠ N208), G236 (= G231), L309 (≠ D304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (≠ S207), D213 (≠ N208)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (= G178), G183 (= G179), G184 (= G180), G185 (= G181), M186 (≠ L182), G236 (= G231), V237 (= V232), T282 (≠ A278), S310 (= S305), G311 (= G306)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A76), G85 (≠ A80), Q86 (= Q81), I101 (= I96), K111 (= K106), I115 (≠ V110), Y118 (≠ R113)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
36% identity, 58% coverage: 21:311/504 of query aligns to 23:316/323 of 7nbfAAA

query
sites
7nbfAAA

T
|
T

P
|
P

L

V

Q
x
L

P
x
T

A

S

R

S

Q

I

L

L

S

N

E

Q

R

L

I

T

G

G

N

R

Q

N

I

L

L

F

L

F

K

K

R

C

E

E

D

L

L
x
F

Q

Q

P

K

V

T

F

G

S

S

F
|
F

K
|
K

V

I

R

R

G

G

A

A

Y

L

N

N

K

A

L

V

A

R

Q

S

L

L

S

V

A

P

E

D

E

A

L

L

A

E

R

R

-

K

-

P

-

K

G

A

V

V

V

V

T

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

A

A

K

K

Q

L

L

E

G

G

I

I

K

P

A

A

T

Y

I

I

V

V

M

V

P

P

R

Q

T

T

T

A

P

P

E

D

L

C

K

K

V

K

Q

L

G

A

V

I

R

Q

A

A

R

Y

G

G

G

A

K

S

V

I

V

V

L

Y

H

C

G

E

D

P

A

S

F

D

P

E

E

S

A

R

L

E

A

N

Y

V

S

A

L

K

K

R

L

V

V

T

E

E

E

E

K

T

G

E

Y

G

V

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

P

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

M

L

E

E

I

V

L

L

R

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

D

D

A

A

I

L

F

V

V

V

P

P

V

V

G
|
G

G
|
G

G
|
G

G
|
G

L
x
M

V

L

A

A

G

G

I

I

A

A

A

I

Y

T

V

V

K

K

Y

A

L

L

Y

K

P

P

Q

S

T

V

K

K

V

V

I

Y

G

A

V

A

E
|
E

P

P

D

S

D

N

S
x
A

-

D

N
x
D

C

C

L

Y

Q

Q

A

S

A

K

M

L

A

K

A

G

G

K

E

L

R

M

V

P

V

N

L

L

E

Y

Q

P

V

P

G

E

L

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

I

I

G

G

Q

L

H
x
N

T

T

F

W

E

P

I

I

C

I

R

R

H

D

Y

L

V

V

D

D

E

D

V

I

I

F

T

T

V

V

S

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

I

T

K

Q

D

L

I

V

Y

W

D

E

D

R

T

M

R

K

S

L

I

L

T

I

E

E

P

P

A
x
T

G

A

A

G

L

V

S

G

V

V

A

A

G

A

I

V

K

L

K

S

Y

Q

V

-

E

H

R

F

E

Q

G

T

V

V

S

S

G

P

Q

E

V

V

-

K

-

N

L

I

V

C

G

I

I

V

D
x
L

S
|
S

G
|
G

A

G

N

N

V

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (≠ S207), D213 (≠ N208), G236 (= G231), L309 (≠ D304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (≠ S207), D213 (≠ N208)
binding magnesium ion: N244 (≠ H240)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (= G178), G183 (= G179), G184 (= G180), G185 (= G181), M186 (≠ L182), G236 (= G231), V237 (= V232), T282 (≠ A278), S310 (= S305), G311 (= G306)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: T23 (= T21), P24 (= P22), L26 (≠ Q24