SitesBLAST

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
38% identity, 62% coverage: 3:318/508 of query aligns to 10:322/326 of 2gn2A

query
sites
2gn2A

E

E

E

D

I

I

L

L

-

E

-

A

R

K

V

R

L

L

T

A

A

G

P

K

V

I

Y

Y

D

-

V

-

A

-

S

-

E

K

T

T

P

G

L

M

E

P

V

R

A

S

P

N

L

Y

L

F

S

S

K

E

R

R

L

C

Q

K

N

G

K

E

V

I

W

F

L

L

K

K

R

F

E

E

D

N

L

M

Q

Q

P
x
R

V
x
T

F
x
G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

Y

F

N

N

C

K

M

L

V

S

H

S

L

L

T

T

D

E

E

A

Q

E

K

K

K

R

A

K

G

G

V

V

I

V

A

A

A

C

S

S

A
|
A

G

G

N

N

H

H

A

A

Q

Q

G

G

V

V

A

S

L

L

S

S

A

C

S

A

K

M

M

L

G

G

I

I

D

D

A

G

K

K

I

V

V

V

M

M

P

P

Q

K

T

G

T

A

P

P

P

K

I

S

K

K

V

V

N

A

A
|
A

V

T

R

C

N
x
D

L
x
Y

G

S

G

A

N

E

V

V

I

V

L

L

H

H

G

G

D

D

T

N

Y

F

D

N

E

D

A

T

S

I

K

A

F

K

A

V

K

S

Q

E

L

I

V

V

A

E

S

T

E

E

Q

G

R

R

T

I

Y

F

I

I

H

P

P

P

Y

Y

D

D

L

P

D

K

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

G

L

L

E

E

M

I

L

M

R

E

Q

D

H

-

S

-

G

-

A

L

F

Y

D

D

V

V

-

D

-

N

I

V

F

I

V

V

C

P

V

I

G

G

L

L

I

I

S

A

G

G

I

I

A

A

S

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A

I

I

K

K

Q

S

V

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S

N

P

P

K

T

T

I

R

K

I

V

I

I

G

G

V

V

E
x
Q

P

A

E

E

D

N

A
x
V

A

H

S
x
G

M

M

T

A

E

A

A

S

L

Y

K

Y

A

T

G

G

E

E

R

I

I

T

V

T

L

H

D

R

Q

T

V

T

G

G

I

T

F

L

A

A

D

D

G
|
G

V

C

A

D

V

V

A

S

Q

R

V

P

G

G

E

N

I

L

P

T

Y

Y

R

E

I

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A

V

Q

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T

E

C

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V

D

D

E

D

M

I

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L

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V

K

S

T

E

D

D

E

E

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C

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A

N

A

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V

M

K

I

D

A

I

L

F

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E

Q

D

R

T

N

R

K

A

V

I

I

A

T

E

E

P

G

A

A

G

G

A

A

L

L

A

A

V

C

A

A

G

A

M

L

K

L

K

S

F

G

V

K

E

L

Q

D

Y

S

S

H

V

I

S

Q

G

N

L

R

E

K

M

T

A

V

A

S

I

I

V
x
I

S
|
S

G

G

A

G

N
|
N

M

I

N

D

F

L

D

S

R

R

L

V

R

S

H

Q

I

I

S

T

active site: K56 (= K51), A81 (= A76), Q207 (≠ E203), V211 (≠ A207), G213 (≠ S209), G235 (= G231), I308 (≠ V304), S309 (= S305)
binding cytidine-5'-monophosphate: R51 (≠ P46), T52 (≠ V47), G53 (≠ F48), A114 (= A109), D117 (≠ N112), Y118 (≠ L113), N312 (= N308)

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)
35% identity, 61% coverage: 10:317/508 of query aligns to 5:320/323 of O59791

query
sites
O59791

L

L

T

V

A

L

P

P

V

T

Y

Y

D

D

-

D

-

V

-

A

-

S

-

A

-

S

-

E

-

R

-

I

-

K

V

F

A

A

S

N

E

K

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

T

L

V

S

N

K

K

R

E

L

F

Q

V

N

A

K

E

V

V

W

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

L

F

R

R

G

G

A

A

Y

L

N

N

C

A

M

L

V

S

H

Q

L

L

T

N

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

L

A

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

S

S

A

A

S

K

K

I

M

L

G

G

I

I

D

P

A

A

K

K

I

I

V

I

M

M

P

P

Q

L

T

D

T

A

P

P

P

E

I

A

K

K

V

V

N

A

A

A

V

T

R

K

N

G

L

Y

G

G

N

Q

V

V

I

I

L

M

H

Y

G

D

D

R

T

Y

Y

K

D

D

E

D

A

R

S

E

K

K

F

M

A

A

K

K

Q

E

L

I

V

S

A

E

S

R

E

E

Q

G

R

L

T

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

L

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

M

L

L

F

R

E

Q

E

H

-

S

V

G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

C

V

L

G
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G

L
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L

I

L

S

S

G

G

I

S

A

A

S

L

V

A

I

A

K

R

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H

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S

A

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P

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N

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C

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Y

G

G

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V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

T

Q

E

Q

A

S

L

F

K

R

A

K

G

G

E

S

R

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I

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V

H

L

I

D

D

Q

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P

G

K

I

T

F

I

A

A

D

D

G

G

V

A

A

Q

V

T

A

Q

Q

H

V

L

G

G

E

N

I

Y

P

T

Y

F

R

S

I

I

A

I

Q

K

T

E

C

K

V

V

D

D

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

E

E

E

I

L

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I

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D

A

C

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L

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K

D

F

I

Y

F

A

E

A

D

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M

R

K

A

I

I

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A

V

E

E

P

P

A

T

G

G

A

C

L

L

A

S

V

F

A

A

G

A

M

A

K

R

K

A

F

M

V

K

E

E

Q

K

Y

-

S

-

V

L

S

K

G

N

L

K

E

R

M

I

A

G

A

I

I

I

V

I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

K57 (= K51) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ A76) 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 (= N78) binding pyridoxal 5'-phosphate
G183 (= G178) binding pyridoxal 5'-phosphate
G184 (= G179) binding pyridoxal 5'-phosphate
G185 (= G180) binding pyridoxal 5'-phosphate
G186 (= G181) binding pyridoxal 5'-phosphate
L187 (= L182) binding pyridoxal 5'-phosphate
E208 (= E203) binding Mg(2+)
G212 (≠ A207) binding Mg(2+)
D214 (≠ S209) binding Mg(2+)
S308 (= S305) binding pyridoxal 5'-phosphate

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
35% identity, 61% coverage: 10:317/508 of query aligns to 1:316/319 of 2zr8A

query
sites
2zr8A

L

L

T

V

A

L

P

P

V

T

Y

Y

D

D

-

D

-

V

-

A

-

S

-

A

-

S

-

E

-

R

-

I

-

K

V

F

A

A

S

N

E

K

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

T

L

V

S

N

K

K

R

E

L

F

Q

V

N

A

K

E

V

V

W

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

L

F

R

R

G

G

A

A

Y

L

N

N

C

A

M

L

V

S

H

Q

L

L

T

N

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

L

A

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

S

S

A

A

S

K

K

I

M

L

G

G

I

I

D

P

A

A

K

K

I

I

V

I

M

M

P

P

Q

L

T

D

T

A

P

P

P

E

I

A

K

K

V

V

N

A

A

A

V

T

R

K

N

G

L

Y

G

G

N

Q

V

V

I

I

L

M

H

Y

G

D

D

R

T

Y

Y

K

D

D

E

D

A
x
R

S

E

K

K

F

M

A

A

K

K

Q

E

L

I

V

S

A

E

S

R

E

E

Q

G

R

L

T

T

Y

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

L

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

M

L

L

F

R

E

Q

E

H

-

S

V

G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

S

L

V

A

I

A

K

R

Q

H

V

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S

A

P

P

K

N

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R

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I

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

T

Q

E

Q

A

S

L

F

K

R

A

K

G

G

E

S

R

I

I

V

V

H

L

I

D

D

Q

T

V

P

G

K

I

T

F

I

A

A

D
|
D

G
|
G

V
x
A

A
x
Q

V
x
T

A

Q

Q

H

V

L

G

G

E

N

I

Y

P

T

Y

F

R

S

I

I

A

I

Q

K

T

E

C

K

V

V

D

D

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

A

S

V

F

A

A

G

A

M

A

K

R

K

A

F

M

V

K

E

E

Q

K

Y

-

S

-

V

L

S

K

G

N

L

K

E

R

M

I

A

G

A

I

I

I

V
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K53 (= K51), S78 (≠ A76), E204 (= E203), G208 (≠ A207), D210 (≠ S209), G232 (= G231), I303 (≠ V304), S304 (= S305)
binding magnesium ion: E204 (= E203), G208 (≠ A207), D210 (≠ S209)
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)
35% identity, 61% coverage: 10:317/508 of query aligns to 1:316/319 of 2zpuA

query
sites
2zpuA

L

L

T

V

A

L

P

P

V

T

Y

Y

D

D

-

D

-

V

-

A

-

S

-

A

-

S

-

E

-

R

-

I

-

K

V

F

A

A

S

N

E

K

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

T

L

V

S

N

K

K

R

E

L

F

Q

V

N

A

K

E

V

V

W

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

L

F

R

R

G

G

A

A

Y

L

N

N

C

A

M

L

V

S

H

Q

L

L

T

N

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

L

A

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

S

S

A

A

S

K

K

I

M

L

G

G

I

I

D

P

A

A

K

K

I

I

V

I

M

M

P

P

Q

L

T

D

T

A

P

P

P

E

I

A

K

K

V

V

N

A

A

A

V

T

R

K

N

G

L

Y

G

G

N

Q

V

V

I

I

L

M

H

Y

G

D

D

R

T

Y

Y

K

D

D

E

D

A

R

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E

K

K

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M

A

A

K

K

Q

E

L

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V

S

A

E

S

R

E

E

Q

G

R

L

T

T

Y

I

I

I

H

P

P
|
P

Y

Y

D

D

D

H

L

P

D

H

V

V

I

L

A

A

G

G

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Q

G

G

T

T

I

A

A

A

L

K

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E

M

L

L

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R

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Q

E

H

-

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G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

S

L

V

A

I

A

K

R

Q

H

V

F

S

A

P

P

K

N

T

C

R

E

I

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

T

Q

E

Q

A

S

L

F

K

R

A

K

G

G

E

S

R

I

I

V

V

H

L

I

D

D

Q

T

V

P

G

K

I

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

V

L

G

G

E

N

I

Y

P

T

Y

F

R

S

I

I

A

I

Q

K

T

E

C

K

V

V

D

D

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

A

S

V

F

A

A

G

A

M

A

K

R

K

A

F

M

V

K

E

E

Q

K

Y

-

S

-

V

L

S

K

G

N

L

K

E

R

M

I

A

G

A

I

I

I

V
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K53 (= K51), S78 (≠ A76), E204 (= E203), G208 (≠ A207), D210 (≠ S209), G232 (= G231), I303 (≠ V304), S304 (= S305)
binding magnesium ion: E204 (= E203), G208 (≠ A207), D210 (≠ S209)
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, 59% coverage: 18:317/508 of query aligns to 19:315/318 of 1wtcA

query
sites
1wtcA

A

A

S
x
N

E

K

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

T

L

V

S

N

K

K

R

E

L

F

Q

V

N

A

K

E

V

V

W

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

L

F

R

R

G

G

A

A

Y

L

N

N

C

A

M

L

V

S

H

Q

L

L

T

N

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

L

A

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

S

S

A

A

S

K

K

I

M

L

G

G

I

I

D

P

A

A

K

K

I

I

V

I

M

M

P

P

Q

L

T

D

T

A

P

P

P

E

I

A

K

K

V

V

N
x
A

A
|
A

V

T

R

K

N

G

L
x
Y

G

G

N

Q

V

V

I

I

L

M

H

Y

G

D

D

R

T

Y

Y

K

D

D

E

D

A

R

S

E

K

K

F

M

A

A

K

K

Q

E

L

I

V

S

A

E

S

R

E

E

Q

G

R

L

T

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

L

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

M

L

L

F

R

E

Q

E

H

-

S

V

G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

S

L

V

A

I

A

K

R

Q

H

V

F

S

A

P

P

K

N

T

C

R

E

I

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

T

Q

E

Q

A

S

L

F

K

R

A

K

G

G

E

S

R

I

I

V

V

H

L

I

D

D

Q

T

V

P

G

K

I

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

V

L

G

G

E

N

I

Y

P

T

Y

F

R

S

I

I

A

I

Q

K

T

E

C

K

V

V

D

D

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

A

S

V

F

A

A

G

A

M

A

K

R

K

A

F

M

V

K

E

E

Q

K

Y

-

S

-

V

L

S

K

G

N

L

K

E

R

M

I

A

G

A

I

I

I

V
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K52 (= K51), S77 (≠ A76), E203 (= E203), G207 (≠ A207), D209 (≠ S209), G231 (= G231), I302 (≠ V304), S303 (= S305)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ S19), K47 (≠ P46), M48 (≠ V47), A109 (≠ N108), A110 (= A109), Y114 (≠ L113)
binding magnesium ion: E203 (= E203), G207 (≠ A207), D209 (≠ S209)
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, 59% coverage: 18:317/508 of query aligns to 19:315/318 of 1v71A

query
sites
1v71A

A

A

S

N

E

K

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

T

L

V

S

N

K

K

R

E

L

F

Q

V

N

A

K

E

V

V

W

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

L

F

R

R

G

G

A

A

Y

L

N

N

C

A

M

L

V

S

H

Q

L

L

T

N

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

L

A

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

S

S

A

A

S

K

K

I

M

L

G

G

I

I

D

P

A

A

K

K

I

I

V

I

M

M

P

P

Q

L

T

D

T

A

P

P

P

E

I

A

K

K

V

V

N

A

A

A

V

T

R

K

N

G

L

Y

G

G

N

Q

V

V

I

I

L

M

H

Y

G

D

D

R

T

Y

Y

K

D

D

E

D

A

R

S

E

K

K

F

M

A

A

K

K

Q

E

L

I

V

S

A

E

S

R

E

E

Q

G

R

L

T

T

Y

I

I

I

H

P

P

P

Y

Y

D

D

D

H

L

P

D

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

M

L

L

F

R

E

Q

E

H

-

S

V

G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

S

L

V

A

I

A

K

R

Q

H

V

F

S

A

P

P

K

N

T

C

R

E

I

V

I

Y

G

G

V

V

E
|
E

P

P

E

E

D

A

A
x
G

A

N

S
x
D

M

G

T

Q

E

Q

A

S

L

F

K

R

A

K

G

G

E

S

R

I

I

V

V

H

L

I

D

D

Q

T

V

P

G

K

I

T

F

I

A

A

D

D

G
|
G

V

A

A

Q

V

T

A

Q

Q

H

V

L

G

G

E

N

I

Y

P

T

Y

F

R

S

I

I

A

I

Q

K

T

E

C

K

V

V

D

D

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

E

E

E

I

L

C

I

A

D

A

C

V

L

K

K

D

F

I

Y

F

A

E

A

D

R

T

M

R

K

A

I

I

V

A

V

E
|
E

P

P

A
x
T

G

G

A

C

L

L

A

S

V

F

A

A

G

A

M

A

K

R

K

A

F

M

V

K

E

E

Q

K

Y

-

S

-

V

L

S

K

G

N

L

K

E

R

M

I

A

G

A

I

I

I

V
x
I

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

L

Y

R

A

H

H

I

F

active site: K52 (= K51), S77 (≠ A76), E203 (= E203), G207 (≠ A207), D209 (≠ S209), G231 (= G231), I302 (≠ V304), S303 (= S305)
binding magnesium ion: E203 (= E203), G207 (≠ A207), D209 (≠ S209)
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)

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)
33% identity, 58% coverage: 18:313/508 of query aligns to 20:312/319 of A4F2N8

query
sites
A4F2N8

A

A

S

N

E

R

T

T

P

P

L

V

E

F

V

T

A

S

P

R

L

T

L

L

S

D

K

A

R

E

L

T

Q

G

N

A

K

Q

V

V

W

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

L

F

R

R

G

G

A

A

Y

F

N

N

C

A

M

L

V

S

H

R

L

F

T

D

D

E

E

A

Q

Q

K

R

K

K

A

A

G

G

V

V

I

V

A

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

S

A

A

A

S

R

K

L

M

L

G

Q

I

M

D

P

A

A

K

T

I

I

V

V

M

M

P

P

Q

T

T

D

T

A

P

P

P

A

I

A

K

K

V

V

N

A

A

A

V

T

R

R

N

E

L

Y

G

G

G

A

N

T

V

V

I

V

L

F

H

Y

G

D

D

R

T

I

Y

T

D

E

E

D

A

R

S

E

K

Q

F

I

A

G

K

R

Q

T

L

L

V

A

A

E

S

Q

E

H

Q

G

R

M

T

T

Y

L

I

I

H

P

P

S

Y

Y

D

D

D

H

L

P

D

D

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

I

A

A

A

L

K

E

E

M

L

L

L

R

-

Q

E

H

F

S

T

G

G

A

P

F

L

D

D

V

A

I

L

F

F

V

V

C

G

V

L

G

G

L

M

I

L

S

S

G

G

I

T

A

A

S

L

V

A

I

T

K

R

Q

A

V

L

S

S

P

P

K

D

T

C

R

L

I

L

I

Y

G

G

V

V

E

E

P

P

E

E

D

A

A

G

A

N

S

D

M

G

T

Q

E

R

A

S

L

F

K

Q

A

T

G

G

E

S

R

I

I

V

V

H

L

I

D

D

Q

T

V

P

G

A

I

T

F

I

A

A

D

D

G

G

V

A

A

Q

V

T

A

Q

Q

H

V

L

G

G

E

N

I

H

P

T

Y

F

R

P

I

I

A

I

Q

R

T

E

C

N

V

V

D

N

E

D

M

I

I

L

T

T

V

V

K

S

T

D

D

A

E

E

I

L

C

V

A

E

A

S

V

M

K

R

D

F

I

F

F

M

E

Q

D

R

T

M

R

K

A

M

I

V

A

V

E

E

P

P

A

T

G

G

A

C

L

L

A

G

V

L

A

A

G

A

M

L

K

R

K

N

F

L

V

K

E

Q

Q

Q

Y

F

S

-

V

-

S

R

G

G

L

Q

E

R

M

V

A

G

A

I

I

I

V

V

S

T

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

K

K53 (= K51) 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)
33% identity, 58% coverage: 20:314/508 of query aligns to 37:332/339 of Q7XSN8

query
sites
Q7XSN8

E

K

T

T

P

P

L

V

E

L

V

S

A

S

P

T

L

S

L

I

S

D

K

A

R

I

L

V

Q

G

N

K

K

Q

V

L

W

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

L

I

R

R

G

G

A

A

Y

S

N

N

C

S

M

I

V

F

H

A

L

L

T

D

D

D

E

D

Q

E

K

A

K

S

A

K

G

G

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

R

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

I

P

P

Q

R

T

N

T

A

P

P

P

A

I

C

K

K

V

V

N

D

A

N

V

V

R

K

N

R

L

Y

G

G

N

H

V

I

I

I

L

W

H

S

G

D

D

V

T

S

Y

I

D

E

E

S

A

R

S

E

K

S

F

V

A

A

K

K

Q

R

L

V

V

Q

A

E

S

E

E

T

Q

G

R

A

T

I

Y

L

I

V

H

H

P

P

Y

F

D

N

L

K

D

N

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

I

V

A

S

L

L

E

E

M

L

L

L

R

E

Q

E

H

V

S

P

G

-

A

E

F

I

D

D

V

T

I

I

F

I

V

V

C

P

V

I

G

S

G

G

L

L

I

I

S

S

G

G

I

V

A

A

S

L

V

A

I

A

K

K

Q

A

V

I

S

N

P

P

K

S

T

I

R

R

I

I

I

L

G

A

V

A

E
|
E

P

P

E

K

D

G

A

A

A

D

S
x
D

M

S

T

A

E

Q

A

S

L

K

K

A

A

A

G

G

E

K

R

I

I

I

V

T

L

L

D

P

Q

S

V

T

G

N

I

T

F

I

A

A

D

D

G

G

V

L

A

R

V

-

A

A

Q

F

V

L

G

G

E

D

I

L

P

T

Y

W

R

P

I

V

A

V

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

I

T

V

V

V

K

D

T

D

D

N

E

A

I

I

C

V

A

D

A

A

V

M

K

K

D

M

I

C

F

Y

E

E

D

M

T

L

R

K

A

V

I

A

A

V

E

E

P

P

A

S

G

G

A

A

L

I

A

G

V

L

-

A

A

A

G

A

M

L

K

S

K

D

F

E

V

F

E

K

Q

Q

Y

S

S

S

V

A

-

W

-

H

S

E

G

S

L

S

E

K

M

I

A

G

A

I

I

I

V

V

S

S

G

G

A

G

N

N

M

V

N

D

F

L

D

G

R

V

L

L

E219 (= E203) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ S209) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/322 of 7nbgAAA

query
sites
7nbgAAA

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I
|
I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K
|
K

V

K

N

L

A

A

V
x
I

R

Q

N

A

L
x
Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

-

K

L

L

K

K

A

G

G

K

E

L

R

M

I

P

V

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I

N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

A
x
T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
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 (≠ L113)

5cvcA Structure of maize serine racemase (see paper)
34% identity, 58% coverage: 21:314/508 of query aligns to 22:316/329 of 5cvcA

query
sites
5cvcA

T

T

P

P

L

V

E

M

V

S

A

S

P

T

L

S

L

I

S

D

K

A

R

M

L

V

Q

G

N

K

K

K

V

L

W

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

L

I

R

R

G

G

A

A

Y

S

N

N

C

S

M

I

V

F

H

A

L

L

T

D

D

D

E

E

Q

Q

K

V

K

S

A

K

G

G

V

V

I

V

A

T

A

H

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

A

G

A

V

V

A

A

L

L

S

A

A

A

S

K

K

L

M

R

G

G

I

I

D

P

A

A

K

H

I

I

V

V

M

I

P

P

Q

R

T

N

T

A

P

P

P

A

I

S

K

K

V

V

N

E

A

N

V

V

R

K

N

C

L

Y

G

G

N

H

V

I

I

I

L

W

H

S

G

D

D

A

T

S

Y

I

D

E

E

S

A

R

S

E

K

Y

F

V

A

S

K

K

Q

R

L

V

V

Q

A

E

S

E

E

T

Q

G

R

A

T

V

Y

L

I

I

H

H

P

P

Y

I

D

N

D

S

L

K

D

Y

V

T

I

I

A

S

G

G

Q

Q

G

G

T

T

I

V

A

S

L

L

E

E

M

L

L

L

R

E

Q

Q

H

-

S

V

G

P

A

E

F

I

D

D

V

T

I

I

F

I

V

V

C

P

V

I

G
x
S

G
|
G

L

L

I

I

S

S

G

G

I

V

A

A

S

L

V

A

I

A

K

K

Q

A

V

I

S

N

P

P

K

S

T

I

R

R

I

I

I

L

G

A

V

A

E
|
E

P

P

E

K

D

G

A
|
A

A

D

S
x
D

M

S

T

A

E

Q

A

S

L

K

K

A

A

A

G

G

E

K

R

I

I

I

V

T

L

L

D

P

Q

S

V

T

G

N

I

T

F

I

A

A

D

D

G
|
G

V
x
L

A

R

V

-

A

A

Q

F

V

L

G

G

E

D

I

L

P

T

Y

W

R

P

I

V

A

V

Q

R

T

D

C

L

V

V

D

D

E

D

M

V

I

I

T

V

V

V

K

D

T

D

D

T

E

A

I

I

C

V

A

D

A

A

V

M

K

K

D

M

I

C

F

Y

E

E

D

I

T

L

R

K

A

V

I

A

A

V

E
|
E

P

P

A

S

G

G

A

A

L

I

A

G

V

L

-

A

A

A

G

A

M

L

K

S

K

D

F

E

V

F

E

K

Q

Q

Y

S

S

S

V

A

-

W

-

H

S

E

G

S

L

S

E

K

M

I

A

G

A

I

I

I

V
|
V

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

D

G

R

T

L

L

active site: K52 (= K51), S77 (≠ A76), E203 (= E203), A207 (= A207), D209 (≠ S209), G231 (= G231), V306 (= V304), S307 (= S305)
binding magnesium ion: E203 (= E203), A207 (= A207), D209 (≠ S209)
binding pyridoxal-5'-phosphate: F51 (= F50), K52 (= K51), N79 (= N78), S178 (≠ G178), G179 (= G179), G180 (= G180), G181 (= G181), L232 (≠ V232), E275 (= E276), S307 (= S305), G308 (= G306)

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/320 of 7nbhAAA

query
sites
7nbhAAA

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K
|
K

V

K

N

L

A

A

V
x
I

R

Q

N

A

L
x
Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G

G

L

M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

-

K

L

L

K

K

A

G

G

K

E

L

R

M

I

P

V

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D
|
D

G
|
G

V

V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I

N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P
|
P

A

T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G

G

A

G

N
|
N

M
x
V

N
x
D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A76), G85 (≠ A80), Q86 (= Q81), K111 (= K106), I115 (≠ V110), Y118 (≠ L113), D235 (= D230), P281 (= P277), N313 (= N308), V314 (≠ M309), D315 (≠ N310)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/323 of 7nbfAAA

query
sites
7nbfAAA

T
|
T

P
|
P

L

V

E
x
L

V
x
T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K

K

V

K

N

L

A

A

V

I

R

Q

N

A

L

Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

L

K

K

L

A

K

G

G

E

K

R

L

I

M

V

P

-

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I
x
N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

A
x
T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
binding magnesium ion: N244 (≠ I240)
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 (≠ E24), T27 (≠ V25), F46 (≠ L44)

Sites not aligning to the query:

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/323 of 7nbdAAA

query
sites
7nbdAAA

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K

K

V

K

N

L

A

A

V

I

R

Q

N

A

L

Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

L

K

K

L

A

K

G

G

E

K

R

L

I

M

V

P

-

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I
x
N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F
x
W

E

E

D

R

T

M

R

K

A

L

I
x
L

A

I

E
|
E

P

P

A
x
T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G
|
G

A

G

N

N

M
x
V

N

D

F
x
L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F268), L278 (≠ I274), V314 (≠ M309), L316 (≠ F311)
binding magnesium ion: N244 (≠ I240)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (= G178), G183 (= G179), G184 (= G180), G185 (= G181), M186 (≠ L182), G236 (= G231), V237 (= V232), E280 (= E276), T282 (≠ A278), S310 (= S305), G311 (= G306)

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)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/323 of 7nbcCCC

query
sites
7nbcCCC

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A
x
T

A
x
H

S

S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

L

Y

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K

K

V

K

N

L

A

A

V

I

R

Q

N

A

L

Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I
x
V

H
|
H

P
|
P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

L

K

K

L

A

K

G

G

E

K

R

L

I

M

V

P

-

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I

N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

A
x
T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding biphenyl-4-ylacetic acid: T78 (≠ A73), H79 (≠ A74), H84 (= H79), V148 (≠ I143), H149 (= H144), P150 (= P145)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
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)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 23:316/323 of 7nbcAAA

query
sites
7nbcAAA

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

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

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D

P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A

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

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K

K

V

K

N

L

A

A

V

I

R

Q

N

A

L

Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

V

S

P

G

-

A

L

F

V

D

D

V

A

I

L

F

V

V

V

C

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

S

I

V

T

I

V

K

K

Q

A

V

L

S

K

P

P

K

S

T

V

R

K

I

V

I

Y

G

A

V

A

E
|
E

P

P

E

S

D

N

A
|
A

A

D

S
x
D

M

C

T

Y

E

Q

A

S

L

K

K

L

A

K

G

G

E

K

R

L

I

M

V

P

-

N

L

L

D

Y

Q

P

V

P

G

E

I

T

F

I

A

A

D

D

G
|
G

V
|
V

A

K

V

-

A

S

Q

S

V

I

G

G

E

L

I
x
N

P

T

Y

W

R

P

I

I

A

I

Q

R

T

D

C

L

V

V

D

D

E

D

M

I

I

F

T

T

V

V

K

T

T

E

D

D

E

E

I

I

C

K

A

C

A

A

V

T

K

Q

D

L

I

V

F

W

E

E

D

R

T

M

R

K

A

L

I

L

A

I

E

E

P

P

A
x
T

G

A

A

G

L

V

A

G

V

V

A

A

G

A

-

V

M

L

K

S

K

Q

F

H

V

F

E

Q

Q

T

Y

V

S

S

V

P

S

E

G

V

L

K

E

N

M

I

A

C

A

I

I

V

V
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K51), S81 (≠ A76), E207 (= E203), A211 (= A207), D213 (≠ S209), G236 (= G231), L309 (≠ V304), S310 (= S305)
binding calcium ion: E207 (= E203), A211 (= A207), D213 (≠ S209)
binding magnesium ion: N244 (≠ I240)
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)

Sites not aligning to the query:

binding magnesium ion: 3

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)
31% identity, 57% coverage: 21:311/508 of query aligns to 26:319/340 of Q9GZT4

query
sites
Q9GZT4

T

T

P

P

L

V

E

L

V

T

A
x
S

P
x
S

L
x
I

L

L

S

N

K

Q

R

L

L

T

Q

G

N

R

K

N

V

L

W

F

L

F

K

K

R

C

E

E

D

L

L

F

Q

Q

P
x
K

V
x
T

F

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

Y

L

N

N

C

A

M

V

V

R

H

S

L

L

T

V

D
x
P

-

D

-

A

-

L

E

E

Q

R

K

K

K

P

A

K

G

A

V

V

I

V

A
x
T

A

H

S

S

A

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

S

A

A

A

S

K

K

L

M

E

G

G

I

I

D

P

A

A

K

Y

I

I

V

V

M

V

P

P

Q

Q

T

T

T

A

P

P

P

D

I

C

K

K

V

K

N

L

A

A

V

I

R

Q

N

A

L
x
Y

G

G

G

A

N

S

V

I

I

V

L

Y

H

C

G

E

D

P

T

S

Y

D

D

E

E

S

A

R

S

E

K

N

F

V

A

A

K

K

Q

R

L

V

V

T

A

E

S

E

E

T

Q

E

R

G

T

I

Y

M

I

V

H

H

P

P

Y

N

D

Q

D

E

L

P

D

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

I

I

A

A

L

L

E

E

M

V

L

L

R

N

Q

Q

H

-

S

V

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A

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F

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D
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D

V

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I

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F

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V

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C

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x
M

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G

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I

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A

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A

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x
D

M

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E

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A

S

-

K

L

L

K

K

A

G

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K

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N

L

L

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Y

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I

A

A

D

D

G

G

V

V

A

K

V

-

A

S

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I

G

G

E

L

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x
N

P

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Y

W

R

P

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I

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C

L

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D

D

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D

M

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C

A

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x
K

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S31 (≠ A26) binding ATP
S32 (≠ P27) binding ATP
I33 (≠ L28) binding ATP
K51 (≠ P46) binding ATP
T52 (≠ V47) binding ATP
K56 (= K51) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ D64) binding Ca(2+)
T81 (≠ A73) binding Ca(2+)
N86 (= N78) binding pyridoxal 5'-phosphate
Q89 (= Q81) binding ATP
Y121 (≠ L113) binding ATP
D178 (= D171) binding Mg(2+)
G185 (= G178) binding pyridoxal 5'-phosphate
G186 (= G179) binding pyridoxal 5'-phosphate
G187 (= G180) binding pyridoxal 5'-phosphate
G188 (= G181) binding pyridoxal 5'-phosphate
M189 (≠ L182) binding pyridoxal 5'-phosphate
E210 (= E203) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (= A207) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ S209) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ I240) binding Ca(2+); binding Mg(2+)
K279 (≠ R272) binding ATP
S313 (= S305) binding pyridoxal 5'-phosphate
N316 (= N308) binding ATP

Sites not aligning to the query:

13 binding Mg(2+)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
31% identity, 57% coverage: 21:311/508 of query aligns to 24:312/322 of 3l6bA

query
sites
3l6bA

T

T

P

P

L

V

E

L

V

T

A

S

P

S

L

I

L

L

S

N

K

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F
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F

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R

G

G

A

A

Y

L

N

N

C

A

M

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-

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-

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K

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K

G

A

V

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A

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S
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S

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x
S

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H

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Y

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x
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A

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D

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-

K

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G

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V

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A

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G

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I

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A

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E

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x
T

G

A

A

G

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A

G

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V

A

A

G

A

-

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active site: K54 (= K51), S77 (≠ A76), E203 (= E203), A207 (= A207), D209 (≠ S209), G232 (= G231), T278 (≠ A278), L305 (≠ V304), S306 (= S305)
binding malonate ion: K54 (= K51), S76 (= S75), S77 (≠ A76), N79 (= N78), H80 (= H79), R128 (≠ A127), G232 (= G231)
binding manganese (ii) ion: E203 (= E203), A207 (= A207), D209 (≠ S209)
binding pyridoxal-5'-phosphate: F53 (= F50), K54 (= K51), N79 (= N78), G178 (= G178), G179 (= G179), G180 (= G180), G181 (= G181), M182 (≠ L182), V233 (= V232), E276 (= E276), T278 (≠ A278), S306 (= S305), G307 (= G306)

Query Sequence

>WP_028486307.1 NCBI__GCF_000483485.1:WP_028486307.1
MPEEILRRVLTAPVYDVASETPLEVAPLLSKRLQNKVWLKREDLQPVFSFKLRGAYNCMV
HLTDEQKKAGVIAASAGNHAQGVALSASKMGIDAKIVMPQTTPPIKVNAVRNLGGNVILH
GDTYDEASKFAKQLVASEQRTYIHPYDDLDVIAGQGTIALEMLRQHSGAFDVIFVCVGGG
GLISGIASVIKQVSPKTRIIGVEPEDAASMTEALKAGERIVLDQVGIFADGVAVAQVGEI
PYRIAQTCVDEMITVKTDEICAAVKDIFEDTRAIAEPAGALAVAGMKKFVEQYSVSGLEM
AAIVSGANMNFDRLRHISERTELGEKREAIFAVTIDEEPGSFKRFCELLGGRRAITEFNY
RYADSSRAVVFVGVRTEGGKPEREAILSELAKQGYAVEDMTDNEMAKLHLRYLVGGHAKG
IANELLYRFEFPERPGALLQFLTQMSEEWNISLFHYRNHGAAYGRVLVGVQVPPEQNQAF
ECYLQNLGYTYVNEQENPGYQLFLKPTA

Or try a new SitesBLAST search

SitesBLAST's Database

SitesBLAST's database includes (1) SwissProt entries with experimentally-supported functional features; and (2) protein structures with bound ligands, from the BioLip database.

by Morgan Price, Arkin group
Lawrence Berkeley National Laboratory