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, 80% coverage: 46:318/341 of query aligns to 16:280/326 of 2gn2A

query
sites
2gn2A

K

K

T

R

L

L

T

A

A

G

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K

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Y

D

-

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x
G

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S

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F

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x
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E

active site: K56 (= K90), A81 (= A115), Q207 (= Q245), V211 (≠ S249), G213 (≠ A251), G235 (= G273)
binding cytidine-5'-monophosphate: R51 (≠ P85), T52 (≠ V86), G53 (≠ F87), A114 (= A148), D117 (≠ A151), Y118 (≠ H152)

Sites not aligning to the query:

active site: 308, 309
binding cytidine-5'-monophosphate: 312

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
33% identity, 85% coverage: 50:340/341 of query aligns to 13:297/319 of 2zr8A

query
sites
2zr8A

T

S

A

E

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D

K

V

F

A

A

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N

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K

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N

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N

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K

active site: K53 (= K90), S78 (≠ A115), E204 (≠ Q245), G208 (≠ S249), D210 (≠ A251), G232 (= G273)
binding magnesium ion: E204 (≠ Q245), G208 (≠ S249), D210 (≠ A251)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F89), K53 (= K90), S77 (= S114), S78 (≠ A115), N80 (= N117), H81 (= H118), P147 (= P187), G179 (= G220), G180 (= G221), G181 (= G222), G182 (= G223), G232 (= G273), E277 (= E318), T279 (≠ A320)
binding serine: S78 (≠ A115), R129 (≠ A169), D231 (= D272), G232 (= G273), A233 (≠ T274), Q234 (≠ A275), T235 (≠ V276)

Sites not aligning to the query:

active site: 303, 304
binding n-(5'-phosphopyridoxyl)-d-alanine: 304

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
33% identity, 85% coverage: 50:340/341 of query aligns to 13:297/319 of 2zpuA

query
sites
2zpuA

T

S

A

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E
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P

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x
T

G

G

S

C

L

L

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A

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A

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K

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Y

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K

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K

N

N

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K

active site: K53 (= K90), S78 (≠ A115), E204 (≠ Q245), G208 (≠ S249), D210 (≠ A251), G232 (= G273)
binding magnesium ion: E204 (≠ Q245), G208 (≠ S249), D210 (≠ A251)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F89), K53 (= K90), S77 (= S114), S78 (≠ A115), N80 (= N117), H81 (= H118), P147 (= P187), G179 (= G220), G180 (= G221), G181 (= G222), G182 (= G223), G232 (= G273), E277 (= E318), T279 (≠ A320)

Sites not aligning to the query:

active site: 303, 304
binding n-(5'-phosphopyridoxyl)-d-alanine: 304

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)
33% identity, 85% coverage: 50:340/341 of query aligns to 17:301/323 of O59791

query
sites
O59791

T

S

A

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K

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A

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K

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C

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N

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F

F

K
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K

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R

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G

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A

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N

N

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A

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A
x
S

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G

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N

H

H

A

A

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Q

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L

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A

A

A

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G

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L

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K

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E

E

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G

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C

L

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A

S

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F

A

A

G

A

A

A

K

R

Q

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Y

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A

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M

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K

E

E

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K

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E

K

N

N

Q

K

K57 (= K90) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ A115) 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 (= N117) binding pyridoxal 5'-phosphate
G183 (= G220) binding pyridoxal 5'-phosphate
G184 (= G221) binding pyridoxal 5'-phosphate
G185 (= G222) binding pyridoxal 5'-phosphate
G186 (= G223) binding pyridoxal 5'-phosphate
L187 (= L224) binding pyridoxal 5'-phosphate
E208 (≠ Q245) binding Mg(2+)
G212 (≠ S249) binding Mg(2+)
D214 (≠ A251) binding Mg(2+)

Sites not aligning to the query:

308 binding pyridoxal 5'-phosphate

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
33% identity, 85% coverage: 50:340/341 of query aligns to 12:296/318 of 1wtcA

query
sites
1wtcA

T

S

A

E

R

R

V

I

Y

K

D

K

V

F

A

A

R
x
N

E

K

T

T

E

P

L

V

E

L

R

T

A

S

P

S

Q

T

L

V

S

N

A

K

R

E

L

F

R

V

N

A

P

E

V

V

Y

F

L

F

K

K

R

C

E

E

D

N

N

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

M

L

A

S

H

Q

I

L

P

N

A

E

E

A

A

Q

L

R

T

K

R

A

G

G

V

V

I

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

S

S

A

A

A

K

R

I

M

L

G

G

V

I

K

P

A

A

I

K

I

I

V

I

V

M

P

P

V

L

T

D

T

A

P

P

Q

E

V

A

K

K

V

V

D
x
A

A
|
A

V

T

R

K

A

G

H
x
Y

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

D

E

R

S

Y

Y

K

S

D

D

D

A

R

Y

E

G

K

H

M

A

A

V

K

Q

E

L

I

Q

S

E

E

E

R

R

E

G

G

L

L

T

T

F

I

V

I

H

P

P

P

F

Y

D

D

D

H

P

P

Y

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

S

-

Q

E

H

E

Q

V

G

G

P

P

I

L

H

D

A

A

I

L

F

F

V

V

P

C

I

L

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

A

L

Y

A

V

A

K

R

S

H

V

F

R

A

P

P

E

N

I

C

K

E

V

V

I

Y

G

G

V

V

Q
x
E

T

P

D

E

D

A

S
x
G

C

N

A
x
D

M

G

A

Q

S

S

L

F

K

R

A

K

G

G

E

S

R

I

V

V

T

H

L

I

N

D

E

T

V

P

G

K

L

T

F

I

S

A

D

D

G
|
G

T

A

A

Q

V

T

K

Q

L

H

V

L

G

G

E

N

E

Y

T

T

F

F

R

S

L

I

C

I

S

K

E

E

Y

K

L

V

D

D

V

I

L

L

L

T

V

V

N

S

T

D

D

E

A

E

L

L

C

I

A

D

A

C

I

L

K

K

D

F

V

Y

F

A

Q

A

D

R

T

M

R

K

S

I

V

V

L

V

E
|
E

P

P

A
x
T

G

G

S

C

L

L

A

S

V

F

A

A

G

A

A

A

K

R

Q

-

Y

-

A

A

E

M

R

K

E

E

G

K

V

L

E

K

N

N

Q

K

active site: K52 (= K90), S77 (≠ A115), E203 (≠ Q245), G207 (≠ S249), D209 (≠ A251), G231 (= G273)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ R58), K47 (≠ P85), M48 (≠ V86), A109 (≠ D147), A110 (= A148), Y114 (≠ H152)
binding magnesium ion: E203 (≠ Q245), G207 (≠ S249), D209 (≠ A251)
binding pyridoxal-5'-phosphate: F51 (= F89), K52 (= K90), N79 (= N117), G178 (= G220), G179 (= G221), G180 (= G222), G181 (= G223), G231 (= G273), E276 (= E318), T278 (≠ A320)

Sites not aligning to the query:

active site: 302, 303
binding pyridoxal-5'-phosphate: 303

1v71A Crystal structure of s.Pombe serine racemase
33% identity, 85% coverage: 50:340/341 of query aligns to 12:296/318 of 1v71A

query
sites
1v71A

T

S

A

E

R

R

V

I

Y

K

D

K

V

F

A

A

R

N

E

K

T

T

E

P

L

V

E

L

R

T

A

S

P

S

Q

T

L

V

S

N

A

K

R

E

L

F

R

V

N

A

P

E

V

V

Y

F

L

F

K

K

R

C

E

E

D

N

N

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

M

L

A

S

H

Q

I

L

P

N

A

E

E

A

A

Q

L

R

T

K

R

A

G

G

V

V

I

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

S

S

A

A

A

K

R

I

M

L

G

G

V

I

K

P

A

A

I

K

I

I

V

I

V

M

P

P

V

L

T

D

T

A

P

P

Q

E

V

A

K

K

V

V

D

A

A

A

V

T

R

K

A

G

H

Y

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

D

E

R

S

Y

Y

K

S

D

D

D

A

R

Y

E

G

K

H

M

A

A

V

K

Q

E

L

I

Q

S

E

E

E

R

R

E

G

G

L

L

T

T

F

I

V

I

H

P

P

P

F

Y

D

D

D

H

P

P

Y

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

S

-

Q

E

H

E

Q

V

G

G

P

P

I

L

H

D

A

A

I

L

F

F

V

V

P

C

I

L

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

A

L

Y

A

V

A

K

R

S

H

V

F

R

A

P

P

E

N

I

C

K

E

V

V

I

Y

G

G

V

V

Q
x
E

T

P

D

E

D

A

S
x
G

C

N

A
x
D

M

G

A

Q

S

S

L

F

K

R

A

K

G

G

E

S

R

I

V

V

T

H

L

I

N

D

E

T

V

P

G

K

L

T

F

I

S

A

D

D

G
|
G

T

A

A

Q

V

T

K

Q

L

H

V

L

G

G

E

N

E

Y

T

T

F

F

R

S

L

I

C

I

S

K

E

E

Y

K

L

V

D

D

V

I

L

L

L

T

V

V

N

S

T

D

D

E

A

E

L

L

C

I

A

D

A

C

I

L

K

K

D

F

V

Y

F

A

Q

A

D

R

T

M

R

K

S

I

V

V

L

V

E
|
E

P

P

A
x
T

G

G

S

C

L

L

A

S

V

F

A

A

G

A

A

A

K

R

Q

-

Y

-

A

A

E

M

R

K

E

E

G

K

V

L

E

K

N

N

Q

K

active site: K52 (= K90), S77 (≠ A115), E203 (≠ Q245), G207 (≠ S249), D209 (≠ A251), G231 (= G273)
binding magnesium ion: E203 (≠ Q245), G207 (≠ S249), D209 (≠ A251)
binding pyridoxal-5'-phosphate: F51 (= F89), K52 (= K90), N79 (= N117), G178 (= G220), G179 (= G221), G180 (= G222), G181 (= G223), G231 (= G273), E276 (= E318), T278 (≠ A320)

Sites not aligning to the query:

active site: 302, 303
binding pyridoxal-5'-phosphate: 303, 304

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, 82% coverage: 51:328/341 of query aligns to 29:301/339 of Q7XSN8

query
sites
Q7XSN8

A

A

R

R

V

I

Y

A

D

P

V

Y

A

V

R

H

E

K

T

T

E

P

L

V

E

L

R

S

A

S

P

T

Q

S

L

I

S

D

A

A

R

I

L

V

R

G

N

K

P

Q

V

L

Y

F

L

F

K

K

R

C

E

E

D

C

N

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

M

I

A

F

H

A

I

L

P

D

A

D

E

D

A

E

L

A

T

S

R

K

G

G

V

V

I

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

S

A

A

A

A

K

R

L

M

R

G

G

V

I

K

P

A

A

I

Y

I

I

V

V

V

I

P

P

V

R

T

N

T

A

P

P

Q

A

V

C

K

K

V

V

D

D

A

N

V

V

R

K

A

R

H

Y

G

G

P

-

T

-

V

-

E

H

V

I

Q

W

F

S

G

D

E

V

S

S

Y

I

S

E

D

S

A

R

Y

E

G

S

H

V

A

A

V

K

Q

R

L

V

Q

Q

E

E

R

T

G

G

L

A

T

I

F

L

V

V

H

H

P

P

F

F

D

N

P

K

Y

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

S

-

Q

E

H

E

Q

V

G

P

P

E

I

I

H

D

A

T

I

I

F

I

V

V

P

P

I

I

G

S

G

G

L

L

A

I

A

S

G

G

V

V

A

A

A

L

Y

A

V

A

K

K

S

A

V

I

R

N

P

P

E

S

I

I

K

R

V

I

I

L

G

A

V

A

Q
x
E

T

P

D

K

D

G

S

A

C

D

A
x
D

M

S

A

A

A

Q

S

S

L

K

K

A

A

A

G

G

E

K

R

I

V

I

T

T

L

L

N

P

E

S

V

T

G

N

L

T

F

I

S

A

D

D

G

G

T

L

A

R

V

A

K

-

L

F

V

L

G

G

E

D

E

L

T

T

F

W

R

P

L

V

C

V

S

R

E

D

Y

L

L

V

D

D

V

I

L

I

L

V

V

V

N

D

T

D

D

N

A

A

L

I

C

V

A

D

A

A

I

M

K

K

D

M

V

C

F

Y

Q

E

D

M

T

L

R

K

S

V

V

A

L

V

E

E

P

P

A

S

G

G

S

A

L

I

A

G

V

L

A

A

G

A

A

A

E219 (≠ Q245) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ A251) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

A4F2N8 L-threo-3-hydroxyaspartate ammonia-lyase; L-threo-3-hydroxyaspartate dehydratase; L-THA DH; EC 4.3.1.16 from Pseudomonas sp. (see paper)
32% identity, 86% coverage: 42:334/341 of query aligns to 7:293/319 of A4F2N8

query
sites
A4F2N8

H

H

D

D

Y

V

L

I

K

K

K

A

T

A

L

-

T

-

A

E

R

R

V

L

Y

E

D

G

V

F

A

A

R

N

E

R

T

T

E

P

L

V

E

F

R

T

A

S

P

R

Q

T

L

L

S

D

A

A

R

E

L

T

R

G

N

A

P

Q

V

V

Y

F

L

I

K

K

R

C

E

E

D

N

N

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

M

L

A

S

H

R

I

F

P

D

A

E

E

A

A

Q

L

R

T

K

R

A

G

G

V

V

I

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

S

A

A

A

A

R

R

L

M

L

G

Q

V

M

K

P

A

A

I

T

I

I

V

V

V

M

P

P

V

T

T

D

T

A

P

P

Q

A

V

A

K

K

V

V

D

A

A

A

V

T

R

R

A

E

H

Y

G

G

G

-

P

-

T

-

V

A

E

T

V

V

Q

F

F

Y

G

D

E

R

S

I

Y

T

S

E

D

D

A

R

Y

E

G

Q

H

I

A

G

V

R

Q

T

L

L

Q

A

E

E

E

Q

R

H

G

G

L

M

T

T

F

L

V

I

H

P

P

S

F

Y

D

D

D

H

P

P

Y

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

S

-

Q

E

H

F

Q

T

G

G

P

P

I

L

H

D

A

A

I

L

F

F

V

V

P

G

I

L

G

G

L

M

A

L

A

S

G

G

V

T

A

A

A

L

Y

A

V

T

K

R

S

A

V

L

R

S

P

P

E

D

I

C

K

L

V

L

I

Y

G

G

V

V

Q

E

T

P

D

E

D

A

S

G

C

N

A

D

M

G

A

Q

A

R

S

S

L

F

K

Q

A

T

G

G

E

S

R

I

V

V

T

H

L

I

N

D

E

T

V

P

G

A

L

T

F

I

S

A

D

D

G

G

T

A

A

Q

V

T

K

Q

L

H

V

L

G

G

E

N

E

H

T

T

F

F

R

P

L

I

C

I

S

R

E

E

Y

N

L

V

D

N

D

D

V

I

L

L

L

T

V

V

N

S

T

D

D

A

A

E

L

L

C

V

A

E

A

S

I

M

K

R

D

F

V

F

F

M

Q

Q

D

R

T

M

R

K

S

M

V

V

L

V

E

E

P

P

A

T

G

G

S

C

L

L

A

G

V

L

A

A

G

A

A

L

K

R

Q

N

Y

L

A

K

E

Q

R

Q

K53 (= K90) mutation to A: Loss of enzymatic activity.

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)
35% identity, 74% coverage: 73:326/341 of query aligns to 40:291/340 of Q9GZT4

query
sites
Q9GZT4

R

R

N

N

P

-

V

L

Y

F

L

F

K

K

R

C

E

E

D

L

N

F

Q

Q

P
x
K

V
x
T

F

G

S

S

F

F

K
|
K

V

I

R

R

G

G

A

A

Y

L

N

N

K

A

M

V

A

R

H

S

I

L

P

V

A
x
P

E

D

A

A

L

L

T

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T
|
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

A

K

R

L

M

E

G

G

V

I

K

P

A

A

I

Y

I

I

V

V

P

P

V

Q

T

T

T

A

P

P

Q

D

V

C

K

K

V

K

D

L

A

A

V

I

R

Q

A

A

H
x
Y

G

G

G

A

P

S

T

I

V

V

E

Y

V

C

V

E

Q

P

F

S

G

D

E

E

S

S

Y

R

S

E

D

N

A

V

Y

-

G

-

H

-

A

A

V

K

Q

R

L

V

Q

T

E

E

R

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

Y

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

S

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

H
x
D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

Y

T

V

V

K

K

S

A

V

L

R

K

P

P

E

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

T

P

D

S

-

N

-
x
A

D

D

S
x
D

C

C

A

-

M

Y

A

Q

A

S

S

K

L

L

K

K

A

G

G

K

E

L

R

M

V

P

T

N

L

L

N

Y

E

P

V

P

G

E

L

T

F

I

S

A

D

D

G

G

T

V

A

K

V

S

K

S

L

-

V

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

S

R

E

D

Y

L

L

V

D

D

V

I

L

F

L

T

V

V

N

T

T

E

D

D

A

E

L

I

C

K

A

C

A

A

I

T

K

Q

D

L

V

V

F

W

Q

E

D

R

T

M

R
x
K

S

L

V

L

L

I

E

E

P

P

A

T

G

A

S

G

L

V

A

G

V

V

A

A

K51 (≠ P85) binding ATP
T52 (≠ V86) binding ATP
K56 (= K90) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ A103) binding Ca(2+)
T81 (= T112) binding Ca(2+)
N86 (= N117) binding pyridoxal 5'-phosphate
Q89 (= Q120) binding ATP
Y121 (≠ H152) binding ATP
D178 (≠ H213) binding Mg(2+)
G185 (= G220) binding pyridoxal 5'-phosphate
G186 (= G221) binding pyridoxal 5'-phosphate
G187 (= G222) binding pyridoxal 5'-phosphate
G188 (= G223) binding pyridoxal 5'-phosphate
M189 (≠ L224) binding pyridoxal 5'-phosphate
E210 (≠ Q245) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (vs. gap) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ S249) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ E282) binding Ca(2+); binding Mg(2+)
K279 (≠ R314) binding ATP

Sites not aligning to the query:

13 binding Mg(2+)
31 binding ATP
32 binding ATP
33 binding ATP
313 binding pyridoxal 5'-phosphate
316 binding ATP

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
35% identity, 74% coverage: 73:326/341 of query aligns to 37:288/320 of 7nbhAAA

query
sites
7nbhAAA

R

R

N

N

P

-

V

L

Y

F

L

F

K

K

R

C

E

E

D

L

N

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

M

V

A

R

H

S

I

L

P

V

A

P

E

D

A

A

L

L

T

E

R

R

-

K

-

P

-

K

G

A

V

V

I

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

S

A

A

A

A

K

R

L

M

E

G

G

V

I

K

P

A

A

I

Y

I

I

V

V

P

P

V

Q

T

T

T

A

P

P

Q

D

V

C

K
|
K

V

K

D

L

A

A

V
x
I

R

Q

A

A

H
x
Y

G

G

G

A

P

S

T

I

V

V

E

Y

V

C

V

E

Q

P

F

S

G

D

E

E

S

S

Y

R

S

E

D

N

A

V

Y

-

G

-

H

-

A

A

V

K

Q

R

L

V

Q

T

E

E

R

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

Y

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

S

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

H

D

A

A

I

L

F

V

V

V

P

P

I

V

G

G

L

M

A

L

A

A

G

G

V

I

A

A

A

I

Y

T

V

V

K

K

S

A

V

L

R

K

P

P

E

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

T

P

D

S

-

N

-
x
A

D

D

S
x
D

C

C

A

-

M

Y

A

Q

A

S

S

K

L

L

K

K

A

G

G

K

E

L

R

M

V

P

T

N

L

L

N

Y

E

P

V

P

G

E

L

T

F

I

S

A

D
|
D

G
|
G

T

V

A

K

V

S

K

S

L

-

V

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

S

R

E

D

Y

L

L

V

D

D

V

I

L

F

L

T

V

V

N

T

T

E

D

D

A

E

L

I

C

K

A

C

A

A

I

T

K

Q

D

L

V

V

F

W

Q

E

D

R

T

M

R

K

S

L

V

L

L

I

E

E

P
|
P

A

T

G

A

S

G

L

V

A

G

V

V

A

A

active site: K53 (= K90), S81 (≠ A115), E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249), G236 (= G273)
binding calcium ion: E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A115), G85 (≠ A119), Q86 (= Q120), K111 (= K145), I115 (≠ V149), Y118 (≠ H152), D235 (= D272), P281 (= P319)

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)
35% identity, 74% coverage: 73:326/341 of query aligns to 37:288/322 of 7nbgAAA

query
sites
7nbgAAA

R

R

N

N

P

-

V

L

Y

F

L

F

K

K

R

C

E

E

D

L

N

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

M

V

A

R

H

S

I

L

P

V

A

P

E

D

A

A

L

L

T

E

R

R

-

K

-

P

-

K

G

A

V

V

I

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

S

A

A

A

A

K

R

L

M

E

G

G

V

I

K

P

A

A

I

Y

I
|
I

V

V

P

P

V

Q

T

T

T

A

P

P

Q

D

V

C

K
|
K

V

K

D

L

A

A

V
x
I

R

Q

A

A

H
x
Y

G

G

G

A

P

S

T

I

V

V

E

Y

V

C

V

E

Q

P

F

S

G

D

E

E

S

S

Y

R

S

E

D

N

A

V

Y

-

G

-

H

-

A

A

V

K

Q

R

L

V

Q

T

E

E

R

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

Y

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

S

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

H

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

Y

T

V

V

K

K

S

A

V

L

R

K

P

P

E

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

T

P

D

S

-

N

-
x
A

D

D

S
x
D

C

C

A

-

M

Y

A

Q

A

S

S

K

L

L

K

K

A

G

G

K

E

L

R

M

V

P

T

N

L

L

N

Y

E

P

V

P

G

E

L

T

F

I

S

A

D

D

G
|
G

T
x
V

A

K

V

S

K

S

L

-

V

I

G

G

E

L

E

N

T

T

F

W

R

P

L

I

C

I

S

R

E

D

Y

L

L

V

D

D

V

I

L

F

L

T

V

V

N

T

T

E

D

D

A

E

L

I

C

K

A

C

A

A

I

T

K

Q

D

L

V

V

F

W

Q

E

D

R

T

M

R

K

S

L

V

L

L

I

E

E

P

P

A
x
T

G

A

S

G

L

V

A

G

V

V

A

A

active site: K53 (= K90), S81 (≠ A115), E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249), G236 (= G273)
binding calcium ion: E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249)
binding pyridoxal-5'-phosphate: F52 (= F89), K53 (= K90), N83 (= N117), G182 (= G220), G183 (= G221), G184 (= G222), G185 (= G223), M186 (≠ L224), G236 (= G273), V237 (≠ T274), T282 (≠ A320)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A115), G85 (≠ A119), Q86 (= Q120), I101 (= I135), K111 (= K145), I115 (≠ V149), Y118 (≠ H152)

Sites not aligning to the query:

active site: 309, 310
binding pyridoxal-5'-phosphate: 310, 311

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
35% identity, 74% coverage: 73:326/341 of query aligns to 37:288/323 of 7nbfAAA

query
sites
7nbfAAA

R

R

N

N

P

-

V

L

Y

F

L

F

K

K

R

C

E

E

D

L

N
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

M

V

A

R

H

S

I

L

P

V

A

P

E

D

A

A

L

L

T

E

R

R

-

K

-

P

-

K

G

A

V

V

I

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

S

A

A

A

A

K

R

L

M

E

G

G

V

I

K

P

A

A

I

Y

I

I

V

V

P

P

V

Q

T

T

T

A

P

P

Q

D

V

C

K

K

V

K

D

L

A

A

V

I

R

Q

A

A

H

Y

G

G

G

A

P

S

T

I

V

V

E

Y

V

C

V

E

Q

P

F

S

G

D

E

E

S

S

Y

R

S

E

D

N

A

V

Y

-

G

-

H

-

A

A

V

K

Q

R

L

V

Q

T

E

E

R

T

G

E

L

G

T

I

F

M

V

V

H

H

P

P

F

N

D

Q

D

E

P

P

Y

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

S

N

Q

Q

H

V

Q

P

G

L

P

-

I

V

H

D

A

A

I

L

F

V

V

V

P

P

I

V

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

Y

T

V

V

K

K

S

A

V

L

R

K

P

P

E

S

I

V

K

K

V

V

I

Y

G

A

V

A

Q
x
E

T

P

D

S

-

N

-
x
A

D

D

S
x
D

C

C

A

-

M

Y

A

Q

A

S

S

K

L

L

K

K

A

G

G

K

E

L

R

M

V

P

T

N

L

L

N

Y

E

P

V

P

G

E

L

T

F

I

S

A

D

D

G
|
G

T
x
V

A

K

V

S

K

S

L

-

V

I

G

G

E

L

E
x
N

T

T

F

W

R

P

L

I

C

I

S

R

E

D

Y

L

L

V

D

D

V

I

L

F

L

T

V

V

N

T

T

E

D

D

A

E

L

I

C

K

A

C

A

A

I

T

K

Q

D

L

V

V

F

W

Q

E

D

R

T

M

R

K

S

L

V

L

L

I

E

E

P

P

A
x
T

G

A

S

G

L

V

A

G

V

V

A

A

active site: K53 (= K90), S81 (≠ A115), E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249), G236 (= G273)
binding calcium ion: E207 (≠ Q245), A211 (vs. gap), D213 (≠ S249)
binding magnesium ion: N244 (≠ E282)
binding pyridoxal-5'-phosphate: F52 (= F89), K53 (= K90), N83 (= N117), G182 (= G220), G183 (= G221), G184 (= G222), G185 (= G223), M186 (≠ L224), G236 (= G273), V237 (≠ T274), T282 (≠ A320)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: F46 (≠ N83)

Sites not aligning to the query:

active site: 309, 310
binding magnesium ion: 3
binding pyridoxal-5'-phosphate: 310, 311
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: 21, 22, 23, 24, 26, 27

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
35% identity, 74% coverage: 73:326/341 of query aligns to 37:288/323 of 7nbdAAA

query
sites
7nbdAAA

R

R

N

N

P

-

V

L

Y

F

L

F

K

K

R

C

E

E

D

L

N

F

Q

Q

P

K

V

T

F

G

S

S

F
|
F