SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing BPHYT_RS11065 FitnessBrowser__BFirm:BPHYT_RS11065 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Or try Sites on a Tree, PaperBLAST, Conserved Domains, or compare to all protein structures

Found 20 (the maximum) hits to proteins with known functional sites (download)

P04968 L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 from Escherichia coli (strain K12) (see paper)
53% identity, 97% coverage: 13:515/516 of query aligns to 15:513/514 of P04968

query
sites
P04968

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K62 (= K60) modified: N6-(pyridoxal phosphate)lysine
N89 (= N87) binding
GGGGL 188:192 (= GGGGL 190:194) binding
S315 (= S317) binding

1tdjA Threonine deaminase (biosynthetic) from e. Coli (see paper)
52% identity, 97% coverage: 13:515/516 of query aligns to 11:493/494 of 1tdjA

query
sites
1tdjA

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active site: K58 (= K60), A83 (= A85), E209 (≠ Q215), S213 (= S219), C215 (≠ A221), G237 (= G243), L310 (≠ T316), S311 (= S317)
binding pyridoxal-5'-phosphate: F57 (= F59), K58 (= K60), N85 (= N87), G184 (= G190), G185 (= G191), G186 (= G192), G187 (= G193), G237 (= G243), E282 (= E288), S311 (= S317), G312 (= G318)

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
37% identity, 60% coverage: 16:326/516 of query aligns to 16:318/326 of 2gn2A

query
sites
2gn2A

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D

V

I

L

V

L

L

V

V

N

S

T

E

D

D

A

E

L

I

C

R

A

N

A

S

I

M

K

I

D

A

V

L

F

I

Q

Q

D

R

T

N

R

K

S

V

V

I

L

T

E

E

P

G

A

A

G

G

S

A

L

L

A

A

V

C

A

A

G

A

A

L

K

L

Q

S

Y

G

A

K

E

L

R

D

E

S

G

H

I

I

E

Q

N

N

Q

R

T

K

L

T

I

V

A

S

I

I

T
x
I

S
|
S

G

G

A

G

N
|
N

M

I

N

D

F

L

D

S

R

R

M

V

active site: K56 (= K60), A81 (= A85), Q207 (= Q215), V211 (≠ S219), G213 (≠ A221), G235 (= G243), I308 (≠ T316), S309 (= S317)
binding cytidine-5'-monophosphate: R51 (≠ P55), T52 (≠ V56), G53 (≠ F57), A114 (= A118), D117 (≠ A121), Y118 (≠ H122), N312 (= N320)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
33% identity, 59% coverage: 20:325/516 of query aligns to 13:312/319 of 2zr8A

query
sites
2zr8A

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

N

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

S

N

A

E

E

A

A

Q

L

R

E

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

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

-

E

D

S

R

Y

Y

S

K

D

D

A

D

Y
x
R

E

E

H

K

A

M

V

A

K

K

L

E

Q

I

K

S

E

E

R

R

D

E

-

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

G
|
G

G
|
G

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

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
x
A

A
x
Q

V
x
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

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

I

L

E

K

N

N

Q

K

T

R

L

I

I

G

A

I

I

I

T
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

active site: K53 (= K60), S78 (≠ A85), E204 (≠ Q215), G208 (≠ S219), D210 (≠ A221), G232 (= G243), I303 (≠ T316), S304 (= S317)
binding magnesium ion: E204 (≠ Q215), G208 (≠ S219), D210 (≠ A221)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F59), K53 (= K60), S77 (= S84), S78 (≠ A85), N80 (= N87), H81 (= H88), P147 (= P157), G179 (= G190), G180 (= G191), G181 (= G192), G182 (= G193), G232 (= G243), E277 (= E288), T279 (≠ A290), S304 (= S317)
binding serine: S78 (≠ A85), R129 (≠ Y140), D231 (= D242), G232 (= G243), A233 (≠ T244), Q234 (≠ A245), T235 (≠ V246)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
33% identity, 59% coverage: 20:325/516 of query aligns to 13:312/319 of 2zpuA

query
sites
2zpuA

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

N

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

S

N

A

E

E

A

A

Q

L

R

E

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

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

-

E

D

S

R

Y

Y

S

K

D

D

A

D

Y

R

E

E

H

K

A

M

V

A

K

K

L

E

Q

I

K

S

E

E

R

R

D

E

-

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

G
|
G

G
|
G

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

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

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

I

L

E

K

N

N

Q

K

T

R

L

I

I

G

A

I

I

I

T
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

active site: K53 (= K60), S78 (≠ A85), E204 (≠ Q215), G208 (≠ S219), D210 (≠ A221), G232 (= G243), I303 (≠ T316), S304 (= S317)
binding magnesium ion: E204 (≠ Q215), G208 (≠ S219), D210 (≠ A221)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F59), K53 (= K60), S77 (= S84), S78 (≠ A85), N80 (= N87), H81 (= H88), P147 (= P157), G179 (= G190), G180 (= G191), G181 (= G192), G182 (= G193), G232 (= G243), E277 (= E288), T279 (≠ A290), S304 (= S317)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
33% identity, 59% coverage: 20:325/516 of query aligns to 12:311/318 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

N

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

S

N

A

E

E

A

A

Q

L

R

E

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

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

-

E

D

S

R

Y

Y

S

K

D

D

A

D

Y

R

E

E

H

K

A

M

V

A

K

K

L

E

Q

I

K

S

E

E

R

R

D

E

-

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

G
|
G

G
|
G

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

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

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

I

L

E

K

N

N

Q

K

T

R

L

I

I

G

A

I

I

I

T
x
I

S
|
S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

active site: K52 (= K60), S77 (≠ A85), E203 (≠ Q215), G207 (≠ S219), D209 (≠ A221), G231 (= G243), I302 (≠ T316), S303 (= S317)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ R28), K47 (≠ P55), M48 (≠ V56), A109 (≠ D117), A110 (= A118), Y114 (≠ H122)
binding magnesium ion: E203 (≠ Q215), G207 (≠ S219), D209 (≠ A221)
binding pyridoxal-5'-phosphate: F51 (= F59), K52 (= K60), N79 (= N87), G178 (= G190), G179 (= G191), G180 (= G192), G181 (= G193), G231 (= G243), E276 (= E288), T278 (≠ A290), S303 (= S317)

1v71A Crystal structure of s.Pombe serine racemase
33% identity, 59% coverage: 20:325/516 of query aligns to 12:311/318 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

N

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

S

N

A

E

E

A

A

Q

L

R

E

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

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

-

E

D

S

R

Y

Y

S

K

D

D

A

D

Y

R

E

E

H

K

A

M

V

A

K

K

L

E

Q

I

K

S

E

E

R

R

D

E

-

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

G
|
G

G
|
G

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

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

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

I

L

E

K

N

N

Q

K

T

R

L

I

I

G

A

I

I

I

T
x
I

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

active site: K52 (= K60), S77 (≠ A85), E203 (≠ Q215), G207 (≠ S219), D209 (≠ A221), G231 (= G243), I302 (≠ T316), S303 (= S317)
binding magnesium ion: E203 (≠ Q215), G207 (≠ S219), D209 (≠ A221)
binding pyridoxal-5'-phosphate: F51 (= F59), K52 (= K60), N79 (= N87), G178 (= G190), G179 (= G191), G180 (= G192), G181 (= G193), G231 (= G243), E276 (= E288), T278 (≠ A290), S303 (= S317), G304 (= G318)

O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
33% identity, 59% coverage: 20:325/516 of query aligns to 17:316/323 of O59791

query
sites
O59791

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

N

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

S

N

A

E

E

A

A

Q

L

R

E

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

G

G

P

-

T

-

V

-

E

Q

V

V

V

I

Q

M

F

Y

G

-

E

D

S

R

Y

Y

S

K

D

D

A

D

Y

R

E

E

H

K

A

M

V

A

K

K

L

E

Q

I

K

S

E

E

R

R

D

E

-

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

G

G

G

G

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

E

T

P

D

E

D

A

S

G

C

N

A

D

M

G

A

Q

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

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

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

I

L

E

K

N

N

Q

K

T

R

L

I

I

G

A

I

I

I

T

I

S

S

G

G

A

G

N

N

M

V

N

D

F

I

D

E

R

R

S82 (≠ A85) mutation to A: Loss of racemase activity. Reduces D-serine dehydratase activity by 99%. Slightly reduced L-serine dehydratase 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)
31% identity, 59% coverage: 21:323/516 of query aligns to 29:329/339 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

N

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

S

D

A

D

E

D

A

E

L

A

E

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

G

G

P

-

T

-

V

-

E

H

V

I

V

I

Q

W

F

S

G

D

E

V

S

S

Y

I

S

E

D

S

A

R

Y

E

E

S

H

V

A

A

V

K

K

R

L

V

Q

Q

K

E

E

E

R

T

D

G

L

A

T

I

F

L

V

V

H

H

P

P

F

F

D

N

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

G

G

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

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

-

L

-

S

-

D

-

E

-

F

K

K

Q

Q

Y

S

A

S

E

A

R

W

E

H

G

-

I

-

E

E

N

S

Q

S

T

K

L

I

I

G

A

I

I

I

T

V

S

S

G

G

A

G

N

N

M

V

N

D

F

L

E219 (≠ Q215) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ A221) 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)
33% identity, 54% coverage: 43:323/516 of query aligns to 37:316/322 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

S

V

A

P

E

D

A

A

L

L

E

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

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

-

V

-

V

-

Q

-

F

Y

G

C

E

E

S

P

Y

S

S

D

D

E

A

S

Y

R

E

E

H

N

A

V

V

A

K

K

-

R

L

V

Q

T

K

E

E

E

R

T

D

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

G
|
G

G
|
G

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

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

G

A

A

V

-

L

K

S

Q

Q

Y

H

A

F

E

Q

R

T

E

V

G

S

I

P

E

E

N

V

Q

K

T

N

L

I

I

C

A

I

I

V

T
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219), G236 (= G243), L309 (≠ T316), S310 (= S317)
binding calcium ion: E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), G182 (= G190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (= G243), V237 (≠ T244), T282 (≠ A290), S310 (= S317), G311 (= G318)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A85), G85 (≠ A89), Q86 (= Q90), I101 (= I105), K111 (= K115), I115 (≠ V119), Y118 (≠ H122)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
33% identity, 54% coverage: 43:323/516 of query aligns to 37:316/323 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

S

V

A

P

E

D

A

A

L

L

E

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

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

-

V

-

V

-

Q

-

F

Y

G

C

E

E

S

P

Y

S

S

D

D

E

A

S

Y

R

E

E

H

N

A

V

V

A

K

K

-

R

L

V

Q

T

K

E

E

E

R

T

D

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

G
|
G

G
|
G

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

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

G

A

A

V

-

L

K

S

Q

Q

Y

H

A

F

E

Q

R

T

E

V

G

S

I

P

E

E

N

V

Q

K

T

N

L

I

I

C

A

I

I

V

T
x
L

S
|
S

G
|
G

A

G

N

N

M

V

N

D

F

L

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219), G236 (= G243), L309 (≠ T316), S310 (= S317)
binding calcium ion: E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219)
binding magnesium ion: N244 (≠ E252)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), G182 (= G190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (= G243), V237 (≠ T244), T282 (≠ A290), S310 (= S317), G311 (= G318)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: F46 (≠ N53)

Sites not aligning to the query:

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
33% identity, 54% coverage: 43:323/516 of query aligns to 37:316/323 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

K
|
K

V

I

R

R

G

G

A

A

Y

L

N

N

K

A

M

V

A

R

H

S

I

L

S

V

A

P

E

D

A

A

L

L

E

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

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

-

V

-

V

-

Q

-

F

Y

G

C

E

E

S

P

Y

S

S

D

D

E

A

S

Y

R

E

E

H

N

A

V

V

A

K

K

-

R

L

V

Q

T

K

E

E

E

R

T

D

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

G
|
G

G
|
G

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

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
x
W

Q

E

D

R

T

M

R

K

S

L

V
x
L

L

I

E
|
E

P

P

A
x
T

G

A

S

G

L

V

A

G

V

V

A

A

G

A

A

V

-

L

K

S

Q

Q

Y

H

A

F

E

Q

R

T

E

V

G

S

I

P

E

E

N

V

Q

K

T

N

L

I

I

C

A

I

I

V

T
x
L

S
|
S

G
|
G

A

G

N

N

M
x
V

N

D

F
x
L

active site: K53 (= K60), S81 (≠ A85), E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219), G236 (= G243), L309 (≠ T316), S310 (= S317)
binding calcium ion: E207 (≠ Q215), A211 (vs. gap), D213 (≠ S219)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F280), L278 (≠ V286), V314 (≠ M321), L316 (≠ F323)
binding magnesium ion: N244 (≠ E252)
binding pyridoxal-5'-phosphate: F52 (= F59), K53 (= K60), N83 (= N87), G182 (= G190), G183 (= G191), G184 (= G192), G185 (= G193), M186 (≠ L194), G236 (= G243), V237 (≠ T244), E280 (= E288), T282 (≠ A290), S310 (= S317), G311 (= G318)

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)
33% identity, 54% coverage: 43:323/516 of query aligns to 37:316/323 of 7nbcCCC

query
sites
7nbcCCC

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

S

V

A

P

E

D

A

A

L

L

E

E

R

R

-

K

-

P

-

K

G

A

V

V

I

V

T
|
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

A

K

R

L

M

E

G

G

V

I

K

P

A

A

I

Y

I

I

V

V

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

-

V

-

V

-

Q

-

F

Y

G

C

E

E

S

P

Y

S

S

D

D

E

A

S

Y

R

E

E

H

N

A

V

V

A

K

K

-

R

L

V

Q

T

K

E

E

E

R

T

D

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

G
|
G

G
|
G

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