SitesBLAST

O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
45% identity, 91% coverage: 4:300/327 of query aligns to 16:312/323 of O59791

query
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O59791

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K57 (= K45) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S70) 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 (= N72) binding pyridoxal 5'-phosphate
G183 (= G171) binding pyridoxal 5'-phosphate
G184 (= G172) binding pyridoxal 5'-phosphate
G185 (= G173) binding pyridoxal 5'-phosphate
G186 (= G174) binding pyridoxal 5'-phosphate
L187 (= L175) binding pyridoxal 5'-phosphate
E208 (= E196) binding Mg(2+)
G212 (≠ R200) binding Mg(2+)
D214 (≠ A202) binding Mg(2+)
S308 (= S296) binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
45% identity, 91% coverage: 4:300/327 of query aligns to 11:307/318 of 1wtcA

query
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1wtcA

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active site: K52 (= K45), S77 (= S70), E203 (= E196), G207 (≠ R200), D209 (≠ A202), G231 (= G224), I302 (≠ L295), S303 (= S296)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ H13), K47 (≠ R40), M48 (≠ V41), A109 (≠ D102), A110 (= A103), Y114 (= Y107)
binding magnesium ion: E203 (= E196), G207 (≠ R200), D209 (≠ A202)
binding pyridoxal-5'-phosphate: F51 (= F44), K52 (= K45), N79 (= N72), G178 (= G171), G179 (= G172), G180 (= G173), G181 (= G174), G231 (= G224), E276 (= E269), T278 (≠ S271), S303 (= S296)

1v71A Crystal structure of s.Pombe serine racemase
45% identity, 91% coverage: 4:300/327 of query aligns to 11:307/318 of 1v71A

query
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1v71A

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active site: K52 (= K45), S77 (= S70), E203 (= E196), G207 (≠ R200), D209 (≠ A202), G231 (= G224), I302 (≠ L295), S303 (= S296)
binding magnesium ion: E203 (= E196), G207 (≠ R200), D209 (≠ A202)
binding pyridoxal-5'-phosphate: F51 (= F44), K52 (= K45), N79 (= N72), G178 (= G171), G179 (= G172), G180 (= G173), G181 (= G174), G231 (= G224), E276 (= E269), T278 (≠ S271), S303 (= S296), G304 (= G297)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
45% identity, 91% coverage: 4:300/327 of query aligns to 12:308/319 of 2zr8A

query
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2zr8A

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active site: K53 (= K45), S78 (= S70), E204 (= E196), G208 (≠ R200), D210 (≠ A202), G232 (= G224), I303 (≠ L295), S304 (= S296)
binding magnesium ion: E204 (= E196), G208 (≠ R200), D210 (≠ A202)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F44), K53 (= K45), S77 (= S69), S78 (= S70), N80 (= N72), H81 (= H73), P147 (= P139), G179 (= G171), G180 (= G172), G181 (= G173), G182 (= G174), G232 (= G224), E277 (= E269), T279 (≠ S271), S304 (= S296)
binding serine: S78 (= S70), R129 (= R121), D231 (= D223), G232 (= G224), A233 (≠ Q225), Q234 (= Q226), T235 (= T227)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
45% identity, 91% coverage: 4:300/327 of query aligns to 12:308/319 of 2zpuA

query
sites
2zpuA

A

A

A

S

R

E

R

R

I

I

A

K

G

K

V

F

A

A

H

N

R

K

T

T

P

P

V

V

L

L

T

T

S

S

G

S

Q

T

L

V

D

N

D

K

R

E

T

F

G

V

A

A

A

E

L

V

F

F

L

F

K

K

A

C

E

E

H

N

L

F

Q

Q

R

K

V

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

T

L

N

N

A

A

V

L

A

S

A

Q

L

L

D

N

T

E

A

A

T

Q

R

R

A

K

R

A

G

G

V

V

V

L

A

T

F

F

S
|
S

G

G

N
|
N

H
|
H

A

A

Q

Q

A

A

V

I

A

A

L

L

T

S

C

A

R

K

I

I

Q

L

Q

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

Q

L

D

D

A

A

P

P

P

E

V

A

K

K

L

V

D

A

A

A

T

T

R

K

G

G

Y

Y

G

G

A

G

E

Q

V

V

V

I

T

M

Y

Y

D

D

R

R

F

Y

T

K

E

D

D

D

R

R

R

E

A

K

I

M

G

A

Q

K

R

E

I

I

A

S

E

E

E

R

R

E

G

G

A

L

T

T

V

I

I

I

P

P

P
|
P

F

Y

D

D

H

H

P

P

D

H

I

V

V

L

A

A

G

G

Q

Q

G

G

T

T

A

A

L

K

E

E

L

L

L

F

E

E

A

E

V

V

P

G

D

P

L

L

D

D

L

A

L

L

V

F

A

V

P

C

I

L

G
|
G

L

L

A

S

G

G

C

S

T

A

A

L

A

A

R

R

G

H

L

F

V

A

P

P

D

N

L

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

P

P

A

E

G

A

R
x
G

H

N

A
x
D

A

G

R

Q

D

Q

A

S

L

F

A

R

R

K

G

G

E

S

V

I

V

V

E

H

V

I

P

D

V

T

P

P

R

K

T

T

V

I

L

A

D

D

G
|
G

Q

A

Q

Q

T

T

A

Q

Y

H

I

L

G

G

A

N

I

Y

P

T

L

F

A

S

V

I

L

I

S

K

H

E

H

K

G

V

V

D

R

D

V

I

V

L

G

T

V

V

E

S

D

D

A

E

A

L

L

I

D

D

T

C

V

L

A

K

W

F

V

Y

A

A

T

A

R

R

M

M

K

K

Q

I

V

V

E
|
E

P

P

S
x
T

G

G

A

C

A

L

A

S

L

F

A

A

L

A

L

R

D

A

G

M

T

K

I

E

D

K

V

L

R

K

G

N

R

K

R

R

V

I

G

G

V

I

L
x
I

S
|
S

G

G

N

N

V

V

active site: K53 (= K45), S78 (= S70), E204 (= E196), G208 (≠ R200), D210 (≠ A202), G232 (= G224), I303 (≠ L295), S304 (= S296)
binding magnesium ion: E204 (= E196), G208 (≠ R200), D210 (≠ A202)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F44), K53 (= K45), S77 (= S69), S78 (= S70), N80 (= N72), H81 (= H73), P147 (= P139), G179 (= G171), G180 (= G172), G181 (= G173), G182 (= G174), G232 (= G224), E277 (= E269), T279 (≠ S271), S304 (= S296)

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)
38% identity, 94% coverage: 1:309/327 of query aligns to 24:336/339 of Q7XSN8

query
sites
Q7XSN8

M

I

H

R

R

E

A

A

A

Q

R

A

R

R

I

I

A

A

G

P

V

Y

A

V

H

H

R

K

T

T

P

P

V

V

L

L

T

S

S

S

G

T

Q

S

L

I

D

D

D

A

R

I

T

V

G

G

A

K

A

Q

L

L

F

F

L

F

K

K

A

C

E

E

H

C

L

F

Q

Q

R

K

V

A

G

G

A

A

F

F

K

K

F

I

R

R

G

G

A

A

T

S

N

N

A

S

V

I

A

F

A

A

L

L

D

D

T

D

A

D

T

E

R

A

A

S

R

K

G

G

V

V

A

T

F

H

S

S

G

G

N

N

H

H

A

A

Q

A

A

A

V

V

A

A

L

L

T

A

C

A

R

K

I

L

Q

R

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

I

P

P

Q

R

D

N

A

A

P

P

P

A

V

C

K

K

L

V

D

D

A

N

T

V

R

K

G

R

Y

Y

G

G

A

G

E

H

V

I

T

W

Y

S

D

D

R

V

F

S

T

I

E

E

D

S

R

R

R

E

A

S

I

V

G

A

Q

K

R

R

I

V

A

Q

E

E

R

T

G

G

A

A

T

I

V

L

I

V

P

H

P

P

F

F

D

N

H

N

P

K

D

N

I

T

V

I

A

S

G

G

Q

Q

G

G

T

T

A

V

A

S

L

L

E

E

L

L

E

E

A

E

V

V

P

P

D

E

L

I

D

D

L

T

L

I

V

I

A

V

P

P

I

I

G

S

G

G

L

L

L

I

A

S

G

G

C

V

T

A

A

L

A

A

R

K

G

A

L

I

V

N

P

P

D

S

L

I

E

R

V

I

V

L

G

A

V

A

E
|
E

P

P

A

K

G

G

R

A

H

D

A
x
D

A

S

R

A

D

Q

A

S

L

K

A

A

R

A

G

G

E

K

V

I

E

T

V

L

P

P

V

S

P

T

R

N

T

T

V

I

L

A

D

D

G

G

Q

L

Q

R

T

-

A

A

Y

F

I

L

G

G

A

D

I

L

P

T

L

W

A

P

V

V

L

V

S

R

H

D

H

L

G

V

V

D

R

D

V

I

G

V

V

V

E

D

D

D

A

N

A

A

A

I

L

V

D

D

T

A

V

M

A

K

W

M

V

C

A

Y

T

E

R

M

M

L

K

K

Q

V

V

A

V

V

E

E

P

P

S

S

G

G

A

A

A

I

A

G

L

L

A

A

L

A

L

L

D

S

G

D

T

E

I

F

D

K

V

Q

-

S

-

A

-

W

-

H

R

E

G

S

R

S

R

K

V

I

G

G

V

I

L

V

S

S

G

G

N

N

V

V

A

D

P

L

A

G

L

V

L

L

A

W

D

E

A

S

L

L

E219 (= E196) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ A202) 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)
39% identity, 91% coverage: 3:300/327 of query aligns to 10:311/329 of 5cvcA

query
sites
5cvcA

R

E

A

A

A

Q

R

A

R

R

I

I

A

A

G

P

V

Y

A

V

H

H

R

R

T

T

P

P

V

V

L

M

T

S

S

S

G

T

Q

S

L

I

D

D

D

A

R

M

T

V

G

G

A

K

L

L

F

F

L

F

K

K

A

C

E

E

H

C

L

F

Q

Q

R

K

V

A

G

G

A

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

T

S

N

N

A

S

V

I

A

F

A

A

L

L

D

D

T

D

A

E

T

Q

R

V

A

S

R

K

G

G

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

A

A

A

V

V

A

A

L

L

T

A

C

A

R

K

I

L

Q

R

Q

G

V

I

P

P

A

A

T

H

I

I

V

V

M

I

P

P

Q

R

D

N

A

A

P

P

P

A

V

S

K

K

L

V

D

E

A

N

T

V

R

K

G

C

Y

Y

G

G

A

G

E

H

V

I

T

W

Y

S

D

D

R

A

F

S

T

I

E

E

D

S

R

R

R

E

A

Y

I

V

G

S

Q

K

R

R

I

V

A

Q

E

E

R

T

G

G

A

A

T

V

V

L

I

I

P

H

P

P

F

I

D

N

H

S

P

K

D

Y

I

T

V

I

A

S

G

G

Q

Q

G

G

T

T

A

V

A

S

L

L

E

E

L

L

E

E

A

Q

V

V

P

P

D

E

L

I

D

D

L

T

L

I

V

I

A

V

P

P

I

I

G
x
S

G
|
G

L

L

L

I

A

S

G

G

C

V

T

A

A

L

A

A

R

K

G

A

L

I

V

N

P

P

D

S

L

I

E

R

V

I

V

L

G

A

V

A

E
|
E

P

P

A

K

G

G

R
x
A

H

D

A
x
D

A

S

R

A

D

Q

A

S

L

K

A

A

R

A

G

G

E

K

V

I

E

T

V

L

P

P

V

S

P

T

R

N

T

T

V

I

L

A

D

D

G
|
G

Q
x
L

Q

R

T

-

A

A

Y

F

I

L

G

G

A

D

I

L

P

T

L

W

A

P

V

V

L

V

S

R

H

D

H

L

G

V

V

D

R

D

V

V

V

I

G

V

V

V

E

D

D

D

A

T

A

A

A

I

L

V

D

D

T

A

V

M

A

K

W

M

V

C

A

Y

T

E

R

I

M

L

K

K

Q

V

V

A

V

V

E
|
E

P

P

S

S

G

G

A

A

A

I

A

G

L

L

A

A

L

A

L

L

D

S

G

D

T

E

I

F

D

K

V

Q

-

S

-

A

-

W

-

H

R

E

G

S

R

S

R

K

V

I

G

G

V

I

L
x
V

S
|
S

G
|
G

G

G

N

N

V

V

active site: K52 (= K45), S77 (= S70), E203 (= E196), A207 (≠ R200), D209 (≠ A202), G231 (= G224), V306 (≠ L295), S307 (= S296)
binding magnesium ion: E203 (= E196), A207 (≠ R200), D209 (≠ A202)
binding pyridoxal-5'-phosphate: F51 (= F44), K52 (= K45), N79 (= N72), S178 (≠ G171), G179 (= G172), G180 (= G173), G181 (= G174), L232 (≠ Q225), E275 (= E269), S307 (= S296), G308 (= G297)

6zspAAA serine racemase bound to atp and malonate. (see paper)
35% identity, 92% coverage: 1:300/327 of query aligns to 9:307/320 of 6zspAAA

query
sites
6zspAAA

M

V

H

E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S
|
S

G
x
S

Q
x
I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L

F

Q

Q

R
x
K

V
x
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

D

-

T

-

A

-

T

-

R

K

A

P

R

K

G

A

V

V

A

T

F

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R
|
R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D

D

L

A

L

L

V

V

A

V

P

P

I

V

G

G

L

M

L

L

A

A

G

G

C

I

T

A

A

I

A

T

A

V

R

K

G

A

L

L

V

K

P

P

D

S

L

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

R
x
A

H

D

A
x
D

A

C

R

Y

D

Q

A

S

L

K

A

L

R

K

G

G

E

K

V

L

V

M

-

P

E

N

V

L

P

Y

V

P

P

P

R

E

T

T

V

I

L

A

D

D

G
|
G

Q

V

Q

K

T
x
S

A

S

Y

I

-

G

I

L

G

N

A

T

I

W

P

P

L

I

A

I

V

R

L

D

S

L

H

V

H

D

G

D

V

I

R

F

V

T

V

V

G

T

V

E

E

D

D

E

A

I

A

K

A

C

L

A

D

T

T

Q

V

L

A

V

W

W

V

-

A

-

T
x
E

R
|
R

M

M

K
|
K

Q

L

V

L

V

I

E

E

P

P

S

T

G

A

A

G

A

V

A

G

L

V

A

A

L

V

L

L

D

S

-

Q

-

H

-

F

G

Q

T

T

I

V

D

S

V

P

R

E

G

V

R

K

R

N

V

I

G

C

V

I

V

V

L
|
L

S
|
S

G

G

N
|
N

V

V

active site: K53 (= K45), S74 (= S70), E200 (= E196), A204 (≠ R200), D206 (≠ A202), G229 (= G224), L302 (= L295), S303 (= S296)
binding adenosine-5'-triphosphate: S28 (= S20), S29 (≠ G21), I30 (≠ Q22), K48 (≠ R40), T49 (≠ V41), Q79 (= Q75), Y111 (= Y107), E266 (≠ T262), R267 (= R263), K269 (= K265), N306 (= N299)
binding magnesium ion: E200 (= E196), A204 (≠ R200), D206 (≠ A202)
binding malonate ion: K53 (= K45), S73 (= S69), S74 (= S70), N76 (= N72), H77 (= H73), R125 (= R121), G229 (= G224), S232 (≠ T227)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
35% identity, 92% coverage: 1:300/327 of query aligns to 10:310/322 of 3l6bA

query
sites
3l6bA

M

V

H

E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

G

S

Q

I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L

F

Q

Q

R

K

V

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

D

-

T

-

A

V

T

R

R

K

A

P

R

K

G

A

V

V

A

T

F

H

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R
|
R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D

D

L

A

L

L

V

V

A

V

P

P

I

V

G
|
G

L
x
M

L

L

A

A

G

G

C

I

T

A

A

I

A

T

A

V

R

K

G

A

L

L

V

K

P

P

D

S

L

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

R
x
A

H

D

A
x
D

A

C

R

Y

D

Q

A

S

L

K

A

L

R

K

G

G

E

K

V

L

V

M

-

P

E

N

V

L

P

Y

V

P

P

P

R

E

T

T

V

I

L

A

D

D

G
|
G

Q
x
V

Q

K

T

S

A

S

Y

I

-

G

I

L

G

N

A

T

I

W

P

P

L

I

A

I

V

R

L

D

S

L

H

V

H

D

G

D

V

I

R

F

V

T

V

V

G

T

V

E

E

D

D

E

A

I

A

K

A

C

L

A

D

T

T

Q

V

L

A

V

W

W

V

-

A

-

T

E

R

R

M

M

K

K

Q

L

V

L

V

I

E
|
E

P

P

S
x
T

G

A

A

G

A

V

A

G

L

V

A

A

L

V

L

L

D

S

-

Q

-

H

-

F

G

Q

T

T

I

V

D

S

V

P

R

E

G

V

R

K

R

N

V

I

G

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

active site: K54 (= K45), S77 (= S70), E203 (= E196), A207 (≠ R200), D209 (≠ A202), G232 (= G224), T278 (≠ S271), L305 (= L295), S306 (= S296)
binding malonate ion: K54 (= K45), S76 (= S69), S77 (= S70), N79 (= N72), H80 (= H73), R128 (= R121), G232 (= G224)
binding manganese (ii) ion: E203 (= E196), A207 (≠ R200), D209 (≠ A202)
binding pyridoxal-5'-phosphate: F53 (= F44), K54 (= K45), N79 (= N72), G178 (= G171), G179 (= G172), G180 (= G173), G181 (= G174), M182 (≠ L175), V233 (≠ Q225), E276 (= E269), T278 (≠ S271), S306 (= S296), G307 (= G297)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 92% coverage: 1:300/327 of query aligns to 9:309/310 of 7nbgDDD

query
sites
7nbgDDD

M

V

H

E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

G

S

Q

I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L

F

Q

Q

R

K

V

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

D

-

T

-

A

V

T

R

R

K

A

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q
|
Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D

D

L

A

L

L

V

V

A

V

P

P

I

V

G
|
G

L
x
M

L

L

A

A

G

G

C

I

T

A

A

I

A

T

A

V

R

K

G

A

L

L

V

K

P

P

D

S

L

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

R
x
A

H

D

A
x
D

A

C

R

Y

D

Q

A

S

L

K

A

L

R

K

G

G

E

K

V

L

V

M

-

P

E

N

V

L

P

Y

V

P

P

P

R

E

T

T

V

I

L

A

D

D

G
|
G

Q
x
V

Q

K

T

S

A

S

Y

I

-

G

I

L

G
x
N

A

T

I

W

P

P

L

I

A

I

V

R

L

D

S

L

H

V

H

D

G

D

V

I

R

F

V

T

V

V

G

T

V

E

E

D

D

E

A

I

A

K

A

C

L

A

D

T

T

Q

V

L

A

V

W

W

V

-

A

-

T

E

R

R

M

M

K

K

Q

L

V

L

V

I

E
|
E

P

P

S
x
T

G

A

A

G

A

V

A

G

L

V

A

A

L

V

L

L

D

S

-

Q

-

H

-

F

G

Q

T

T

I

V

D

S

V

P

R

E

G

V

R

K

R

N

V

I

G

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

active site: K53 (= K45), S76 (= S70), E202 (= E196), A206 (≠ R200), D208 (≠ A202), G231 (= G224), L304 (= L295), S305 (= S296)
binding calcium ion: E202 (= E196), A206 (≠ R200), D208 (≠ A202)
binding magnesium ion: N239 (≠ G231)
binding ortho-xylene: S76 (= S70), Q81 (= Q75), I96 (= I90), Y113 (= Y107)
binding pyridoxal-5'-phosphate: F52 (= F44), K53 (= K45), N78 (= N72), G177 (= G171), G178 (= G172), G179 (= G173), G180 (= G174), M181 (≠ L175), G231 (= G224), V232 (≠ Q225), E275 (= E269), T277 (≠ S271), S305 (= S296), G306 (= G297)

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)
36% identity, 92% coverage: 1:300/327 of query aligns to 12:317/340 of Q9GZT4

query
sites
Q9GZT4

M

V

H
x
E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S
|
S

G
x
S

Q
x
I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L

F

Q

Q

R
x
K

V
x
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

-

V

-
x
P

D

D

T

A

A

L

T

E

R

R

A

K

-

P

R

K

G

A

V

V

A
x
T

F

H

S

S

G

G

N
|
N

H

H

A

G

Q
|
Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y
|
Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D
|
D

L

A

L

L

V

V

A

V

P

P

I

V

G
|
G

L
x
M

L

L

A

A

G

G

C

I

T

A

A

I

A

T

A

V

R

K

G

A

L

L

V

K

P

P

D

S

L

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

R
x
A

H

D

A
x
D

A

C

R

Y

D

Q

A

S

L

K

A

L

R

K

G

G

E

K

V

L

V

M

-

P

E

N

V

L

P

Y

V

P

P

P

R

E

T

T

V

I

L

A

D

D

G

G

Q

V

Q

K

T

S

A

S

Y

I

-

G

I

L

G
x
N

A

T

I

W

P

P

L

I

A

I

V

R

L

D

S

L

H

V

H

D

G

D

V

I

R

F

V

T

V

V

G

T

V

E

E

D

D

E

A

I

A

K

A

C

L

A

D

T

T

Q

V

L

A

V

W

W

V

-

A

-

T

E

R

R

M

M

K
|
K

Q

L

V

L

V

I

E

E

P

P

S

T

G

A

A

G

A

V

A

G

L

V

A

A

L

V

L

L

D

S

-

Q

-

H

-

F

G

Q

T

T

I

V

D

S

V

P

R

E

G

V

R

K

R

N

V

I

G

C

V

I

V

V

L

L

S
|
S

G

G

N
|
N

V

V

E13 (≠ H2) binding Mg(2+)
S31 (= S20) binding ATP
S32 (≠ G21) binding ATP
I33 (≠ Q22) binding ATP
K51 (≠ R40) binding ATP
T52 (≠ V41) binding ATP
K56 (= K45) modified: N6-(pyridoxal phosphate)lysine
P69 (vs. gap) binding Ca(2+)
T81 (≠ A67) binding Ca(2+)
N86 (= N72) binding pyridoxal 5'-phosphate
Q89 (= Q75) binding ATP
Y121 (= Y107) binding ATP
D178 (= D164) binding Mg(2+)
G185 (= G171) binding pyridoxal 5'-phosphate
G186 (= G172) binding pyridoxal 5'-phosphate
G187 (= G173) binding pyridoxal 5'-phosphate
G188 (= G174) binding pyridoxal 5'-phosphate
M189 (≠ L175) binding pyridoxal 5'-phosphate
E210 (= E196) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ R200) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ A202) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ G231) binding Ca(2+); binding Mg(2+)
K279 (= K265) binding ATP
S313 (= S296) binding pyridoxal 5'-phosphate
N316 (= N299) binding ATP

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
36% identity, 92% coverage: 1:300/327 of query aligns to 9:314/323 of 7nbfAAA

query
sites
7nbfAAA

M

V

H

E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H
|
H

R
x
L

T
|
T

P
|
P

V

V

L
|
L

T
|
T

S

S

G

S

Q

I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L
x
F

Q

Q

R

K

V

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

-

V

-

P

D

D

T

A

A

L

T

E

R

R

A

K

-

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D

D

L

A

L

L

V

V

A

V

P

P

I

V

G
|
G

L
x
M

L

L

A

A

G

G

C

I

T

A

A

I

A

T

A

V

R

K

G

A

L

L

V

K

P

P

D

S

L

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

R
x
A

H

D

A
x
D

A

C

R

Y

D

Q

A

S

L

K

A

L

R

K

G

G

E

K

V

L

V

M

-

P

E

N

V

L

P

Y

V

P

P

P

R

E

T

T

V

I

L

A

D

D

G
|
G

Q
x
V

Q

K

T

S

A

S

Y

I

-

G

I

L

G
x
N

A

T

I

W

P

P

L

I

A

I

V

R

L

D

S

L

H

V

H

D

G

D

V

I

R

F

V

T

V

V

G

T

V

E

E

D

D

E

A

I

A

K

A

C

L

A

D

T

T

Q

V

L

A

V

W

W

V

-

A

-

T

E

R

R

M

M

K

K

Q

L

V

L

V

I

E

E

P

P

S
x
T

G

A

A

G

A

V

A

G

L

V

A

A

L

V

L

L

D

S

-

Q

-

H

-

F

G

Q

T

T

I

V

D

S

V

P

R

E

G

V

R

K

R

N

V

I

G

C

V

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

active site: K53 (= K45), S81 (= S70), E207 (= E196), A211 (≠ R200), D213 (≠ A202), G236 (= G224), L309 (= L295), S310 (= S296)
binding calcium ion: E207 (= E196), A211 (≠ R200), D213 (≠ A202)
binding magnesium ion: N244 (≠ G231)
binding pyridoxal-5'-phosphate: F52 (= F44), K53 (= K45), N83 (= N72), G182 (= G171), G183 (= G172), G184 (= G173), G185 (= G174), M186 (≠ L175), G236 (= G224), V237 (≠ Q225), T282 (≠ S271), S310 (= S296), G311 (= G297)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (= H13), L22 (≠ R14), T23 (= T15), P24 (= P16), L26 (= L18), T27 (= T19), F46 (≠ L38)

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)
36% identity, 92% coverage: 1:300/327 of query aligns to 9:314/323 of 7nbdAAA

query
sites
7nbdAAA

M

V

H

E

R

K

A

A

A

H

R

I

R

N

I

I

A

R

G

D

V

S

A

I

H

H

R

L

T

T

P

P

V

V

L

L

T

T

S

S

G

S

Q

I

L

L

D

N

D

Q

R

L

T

T

G

G

A

R

A

N

L

L

F

F

L

F

K

K

A

C

E

E

H

L

L

F

Q

Q

R

K

V

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

A

R

A

S

L

L

-

V

-

P

D

D

T

A

A

L

T

E

R

R

A

K

-

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A

G

Q

Q

A

A

V

L

A

T

L

Y

T

A

C

A

R

K

I

L

Q

E

Q

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

Q

Q

D

T

A

A

P

P

P

D

V

C

K

K

L

K

D

L

A

A

T

I

R

Q

G

A

Y

Y

G

G

A

A

E

S

V

I

V

V

T

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

R

E

A

N

I

V

G

A

Q

K

R

R

I

V

A

T

E

E

R

T

G

E

A

G

T

I

V

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

D

A

I

V

V

I

A

A

G

G

Q

Q

G

G

T

T

A

I

A

A

L

L

E

E

L

V

L

L

E

N

A

Q

V

V

P

P

D

L

L

V

D

D

L

A

L

L

V

V

A

V

P

P

I

V