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)
39% identity, 97% coverage: 7:321/325 of query aligns to 12:321/323 of O59791

query
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O59791

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K57 (= K52) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (= S77) 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 (= N79) binding pyridoxal 5'-phosphate
G183 (= G182) binding pyridoxal 5'-phosphate
G184 (= G183) binding pyridoxal 5'-phosphate
G185 (= G184) binding pyridoxal 5'-phosphate
G186 (= G185) binding pyridoxal 5'-phosphate
L187 (= L186) binding pyridoxal 5'-phosphate
E208 (= E207) binding Mg(2+)
G212 (≠ F211) binding Mg(2+)
D214 (≠ E213) binding Mg(2+)
S308 (= S308) binding pyridoxal 5'-phosphate

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
39% identity, 97% coverage: 7:321/325 of query aligns to 8:317/319 of 2zr8A

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2zr8A

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active site: K53 (= K52), S78 (= S77), E204 (= E207), G208 (≠ F211), D210 (≠ E213), G232 (≠ A236), I303 (≠ L307), S304 (= S308)
binding magnesium ion: E204 (= E207), G208 (≠ F211), D210 (≠ E213)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F51), K53 (= K52), S77 (= S76), S78 (= S77), N80 (= N79), H81 (= H80), P147 (≠ S146), G179 (= G182), G180 (= G183), G181 (= G184), G182 (= G185), G232 (≠ A236), E277 (= E281), T279 (≠ G283), S304 (= S308)
binding serine: S78 (= S77), R129 (= R128), D231 (= D235), G232 (≠ A236), A233 (≠ L237), Q234 (≠ L238), T235 (= T239)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
39% identity, 97% coverage: 7:321/325 of query aligns to 8:317/319 of 2zpuA

query
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2zpuA

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active site: K53 (= K52), S78 (= S77), E204 (= E207), G208 (≠ F211), D210 (≠ E213), G232 (≠ A236), I303 (≠ L307), S304 (= S308)
binding magnesium ion: E204 (= E207), G208 (≠ F211), D210 (≠ E213)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F51), K53 (= K52), S77 (= S76), S78 (= S77), N80 (= N79), H81 (= H80), P147 (≠ S146), G179 (= G182), G180 (= G183), G181 (= G184), G182 (= G185), G232 (≠ A236), E277 (= E281), T279 (≠ G283), S304 (= S308)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
39% identity, 97% coverage: 7:321/325 of query aligns to 7:316/318 of 1wtcA

query
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1wtcA

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V

S

D

G

D

V

I

V

L

A

T

V

V

T

S

D

D

A

E

E

E

V

L

A

I

E

D

A

C

M

L

R

K

Y

F

A

Y

F

A

S

A

T

R

L

M

K

K

L

I

V

V

E
|
E

P

P

G
x
T

G

G

C

C

V

L

A

S

L

F

T

A

A

A

L

R

T

A

G

M

K

K

V

E

D

K

V

L

A

K

G

N

K

K

T

R

V

I

A

G

I

I

V

I

L
x
I

S
|
S

G

G

N

N

V

V

D

D

P

I

G

E

L

R

F

Y

A

A

Q

H

V

F

L

L

active site: K52 (= K52), S77 (= S77), E203 (= E207), G207 (≠ F211), D209 (≠ E213), G231 (≠ A236), I302 (≠ L307), S303 (= S308)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ V20), K47 (≠ R47), M48 (≠ A48), A109 (≠ E109), A110 (≠ G110), Y114 (≠ F114)
binding magnesium ion: E203 (= E207), G207 (≠ F211), D209 (≠ E213)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), G178 (= G182), G179 (= G183), G180 (= G184), G181 (= G185), G231 (≠ A236), E276 (= E281), T278 (≠ G283), S303 (= S308)

1v71A Crystal structure of s.Pombe serine racemase
39% identity, 97% coverage: 7:321/325 of query aligns to 7:316/318 of 1v71A

query
sites
1v71A

D

D

I

V

Q

A

A

S

A

A

A

S

V

E

R

R

L

I

K

K

G

K

S

F

A

A

V

N

E

K

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

T

L

V

N

N

D

K

R

E

L

F

G

V

G

A

R

E

I

V

F

F

L

F

K

K

P

C

E

E

T

N

L

F

Q

Q

R

K

A

M

G

G

A

A

F
|
F

K
|
K

F

F

R

R

G

G

A

A

Y

L

N

N

R

A

L

L

S

S

Q

Q

L

L

S

N

D

E

E

A

E

Q

K

R

A

K

R

A

G

G

V

V

V

L

A

T

F

F

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

L

L

A

S

A

A

R

K

L

I

L

L

G

G

V

I

P

P

A

A

L

K

I

I

V

I

M

M

P

P

S

L

D

D

S

A

P

P

S

E

V

A

K

K

V

V

E

A

G

A

T

T

R

K

G

G

F

Y

G

G

A

G

D

Q

I

V

R

I

F

M

Y

Y

D

D

R

R

F

Y

T

K

E

D

D

D

R

R

V

E

A

K

I

M

A

A

D

K

Q

E

I

I

A

S

A

E

E

R

R

E

G

G

C

L

V

T

V

I

P

P

S

P

Y

Y

D

D

D

H

P

P

H

H

I

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

G

A

L

K

E

E

I

L

V

F

A

E

Q

E

A

V

A

G

A

P

Q

-

G

-

A

-

T

-

L

L

D

D

R

A

L

L

I

F

C

V

C

C

V

L

G
|
G

L

L

I

L

A

S

G

G

T

S

S

A

T

L

A

A

V

A

K

R

A

H

L

F

S

A

P

P

A

N

T

C

E

E

I

V

W

Y

G

G

V

V

E
|
E

P

P

A

E

G

A

F
x
G

D

N

E
x
D

T

G

R

Q

S

S

L

F

E

R

S

K

G

G

R

S

R

I

E

V

T

H

I

I

D

D

K

T

D

-

A

P

R

K

S

T

I

I

C

A

D

D

A
x
G

L

A

L

Q

T

T

P

Q

I

H

P

L

G

G

D

N

L

Y

T

T

W

F

P

S

I

I

N

I

Q

K

K

E

N

K

L

V

S

D

G

D

V

I

V

L

A

T

V

V

T

S

D

D

A

E

E

E

V

L

A

I

E

D

A

C

M

L

R

K

Y

F

A

Y

F

A

S

A

T

R

L

M

K

K

L

I

V

V

E
|
E

P

P

G
x
T

G

G

C

C

V

L

A

S

L

F

T

A

A

A

L

R

T

A

G

M

K

K

V

E

D

K

V

L

A

K

G

N

K

K

T

R

V

I

A

G

I

I

V

I

L
x
I

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

I

G

E

L

R

F

Y

A

A

Q

H

V

F

L

L

active site: K52 (= K52), S77 (= S77), E203 (= E207), G207 (≠ F211), D209 (≠ E213), G231 (≠ A236), I302 (≠ L307), S303 (= S308)
binding magnesium ion: E203 (= E207), G207 (≠ F211), D209 (≠ E213)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), G178 (= G182), G179 (= G183), G180 (= G184), G181 (= G185), G231 (≠ A236), E276 (= E281), T278 (≠ G283), S303 (= S308), G304 (= G309)

Q7XSN8 Serine racemase; D-serine dehydratase; D-serine ammonia-lyase; L-serine dehydratase; L-serine ammonia-lyase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Oryza sativa subsp. japonica (Rice) (see paper)
36% identity, 98% coverage: 5:321/325 of query aligns to 21:336/339 of Q7XSN8

query
sites
Q7XSN8

L

I

A

H

D

S

I

I

Q

R

A

E

A

A

A

Q

V

A

R

R

L

I

K

A

G

P

S

Y

A

V

V

H

E

K

T

T

P

P

L

V

I

L

E

S

S

S

P

T

A

S

L

I

N

D

D

A

R

I

L

V

G

G

G

K

R

Q

I

L

F

F

L

F

K

K

P

C

E

E

T

C

L

F

Q

Q

R

K

A

A

G

G

A

A

F

F

K

K

F

I

R

R

G

G

A

A

Y

S

N

N

R

S

L

I

S

F

Q

A

L

L

S

D

D

D

E

D

E

E

K

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

G

A

V

V

A

A

L

L

A

A

R

K

L

L

L

R

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

I

P

P

S

R

D

N

S

A

P

P

S

A

V

C

K

K

V

V

E

D

G

N

T

V

R

K

G

R

F

Y

G

G

A

G

D

H

I

I

R

I

F

W

Y

S

D

D

R

V

F

S

T

I

E

E

D

S

R

R

V

E

A

S

I

V

A

A

D

K

Q

R

I

V

A

Q

A

E

E

E

R

T

G

G

C

A

V

I

V

L

V

V

P

H

S

P

Y

F

D

N

P

K

H

N

I

T

I

I

A

S

G

G

Q

Q

G

G

T

T

V

V

G

S

L

L

E

E

I

L

V

L

A

E

Q

E

A

V

A

-

Q

-

G

-

A

P

T

E

L

I

D

D

R

T

L

I

I

I

C

V

C

P

V

I

G

S

G

G

L

L

I

I

A

S

G

G

T

V

S

A

T

L

A

A

V

A

K

K

A

A

L

I

S

N

P

P

A

S

T

I

E

R

I

I

W

L

G

A

V

A

E
|
E

P

P

A

K

G

G

F

A

D

D

E
x
D

T

S

R

A

R

Q

S

S

L

K

E

A

S

A

G

G

R

K

R

I

E

I

T

T

I

L

D

-

K

P

D

S

A

T

R

N

S

T

I

I

C

A

D

D

A

G

L

L

L

R

T

A

P

F

I

L

P

-

G

G

D

D

L

L

T

T

W

W

P

P

I

V

N

V

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

A

V

V

V

T

D

D

D

A

N

E

A

V

I

A

V

E

D

A

A

M

M

R

K

Y

M

A

C

F

Y

S

E

T

M

L

L

K

K

L

V

V

A

V

V

E

E

P

P

G

S

G

G

C

A

V

I

A

G

L

L

T

A

A

A

L

L

T

S

G

D

K

E

V

F

D

K

V

Q

A

S

-

S

-

A

-

W

-

H

-

E

G

S

K

S

T

K

V

I

A

G

I

I

V

I

L

V

S

S

G

G

N

N

V

V

D

D

P

L

G

G

L

V

F

L

A

W

Q

E

V

S

L

L

E219 (= E207) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ E213) 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)
37% identity, 97% coverage: 8:321/325 of query aligns to 8:320/329 of 5cvcA

query
sites
5cvcA

I

I

Q

R

A

E

A

A

A

Q

V

A

R

R

L

I

K

A

G

P

S

Y

A

V

V

H

E

R

T

T

P

P

L

V

I

M

E

S

S

S

P

T

A

S

L

I

N

D

D

A

R

M

L

V

G

G

G

K

R

K

I

L

F

F

L

F

K

K

P

C

E

E

T

C

L

F

Q

Q

R

K

A

A

G

G

A

A

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

S

N

N

R

S

L

I

S

F

Q

A

L

L

S

D

D

D

E

E

E

Q

K

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

G

A

V

V

A

A

L

L

A

A

R

K

L

L

L

R

G

G

V

I

P

P

A

A

L

H

I

I

V

V

M

I

P

P

S

R

D

N

S

A

P

P

S

A

V

S

K

K

V

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E

E

G

N

T

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C

F

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G

A

G

D

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F

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D

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T

I

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E

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V

E

A

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I

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K

Q

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I

V

A

Q

A

E

E

E

R

T

G

G

C

A

V

V

V

L

V

I

P

H

S

P

Y

I

D

N

D

S

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K

H

Y

I

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I

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G

Q

Q

G

G

T

T

V

V

G

S

L

L

E

E

I

L

V

L

A

E

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Q

A

V

A

-

Q

-

G

-

A

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T

E

L

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D

D

R

T

L

I

I

I

C

V

C

P

V

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G
x
S

G
|
G

L

L

I

I

A

S

G

G

T

V

S

A

T

L

A

A

V

A

K

K

A

A

L

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N

P

P

A

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T

I

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R

I

I

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L

G

A

V

A

E
|
E

P

P

A

K

G

G

F
x
A

D

D

E
x
D

T

S

R

A

R

Q

S

S

L

K

E

A

S

A

G

G

R

K

R

I

E

I

T

T

I

L

D

-

K

P

D

S

A

T

R

N

S

T

I

I

C

A

D

D

A
x
G

L
|
L

L

R

T

A

P

F

I

L

P

-

G

G

D

D

L

L

T

T

W

W

P

P

I

V

N

V

Q

R

K

D

N

L

L

V

S

D

G

D

V

V

V

I

A

V

V

V

T

D

D

D

A

T

E

A

V

I

A

V

E

D

A

A

M

M

R

K

Y

M

A

C

F

Y

S

E

T

I

L

L

K

K

L

V

V

A

V

V

E
|
E

P

P

G

S

G

G

C

A

V

I

A

G

L

L

T

A

A

A

L

L

T

S

G

D

K

E

V

F

D

K

V

Q

A

S

-

S

-

A

-

W

-

H

-

E

G

S

K

S

T

K

V

I

A

G

I

I

V

I

L
x
V

S
|
S

G
|
G

G

G

N

N

V

V

D

D

P

L

G

G

L

T

F

L

A

W

Q

Q

V

S

L

M

active site: K52 (= K52), S77 (= S77), E203 (= E207), A207 (≠ F211), D209 (≠ E213), G231 (≠ A236), V306 (≠ L307), S307 (= S308)
binding magnesium ion: E203 (= E207), A207 (≠ F211), D209 (≠ E213)
binding pyridoxal-5'-phosphate: F51 (= F51), K52 (= K52), N79 (= N79), S178 (≠ G182), G179 (= G183), G180 (= G184), G181 (= G185), L232 (= L237), E275 (= E281), S307 (= S308), G308 (= G309)

8y1jA Structure of the pyridoxal 5'-phosphate-dependent (plp) threonine deaminase ilva1 from pseudomonas aeruginosa pao1 (see paper)
38% identity, 92% coverage: 14:313/325 of query aligns to 12:309/502 of 8y1jA

query
sites
8y1jA

R

R

L

V

K

Y

G

D

S

V

A

A

V

V

E

E

T

T

P

P

L

L

I

Q

E

P

S

A

P

R

A

Q

L

L

N

S

D

E

R

R

L

L

G

G

G

N

R

Q

I

V

F

L

L

L

K

K

P

R

E

E

T

D

L

L

Q

Q

R

P

A

V

G

F

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

Y

N

N

R

K

L

V

S

A

Q

Q

L

L

S

T

D

E

E

E

K

K

A

A

R

R

G

G

V

V

V

I

A

A

F

A

S
|
S

S

A

G

G

N

N

H
|
H

A

A

Q

Q

G

G

V

L

A

A

L

L

A

A

R

K

L

R

L

Q

G

G

V

I

P

R

A

A

L

V

I

I

V

V

M

M

P

P

S

K

D

T

S

T

P

P

S

E

V

I

K

K

V

V

E

Q

G

A

T

V

R

R

G

A

F

H

G

G

A

A

D

K

I

A

R

V

F

L

Y

H

D

G

R

D

F

A

T

F

E

P

D

E

R

A

V

L

A

A

I

H

A

A

D

L

Q

K

I

L

A

V

A

D

E

E

R

K

G

G

C

Y

V

T

V

F

V

V

P

H

S

P

Y

Y

D

D

P

P

H

D

I

T

I

I

A

A

G

G

Q

Q

G

G

T

T

V

V

G

A

L

M

E

E

I

I

V

L

A

R

Q

Q

A

-

Q

Q

G

P

A

G

T

R

L

L

D

D

R

A

L

I

I

F

C

V

C

P

V

V

G

G

L

L

I

V

A

A

G

G

T

I

S

A

T

A

A

Y

V

V

K

K

A

Y

L

L

S

R

P

P

A

E

T

I

E

K

I

V

W

I

G

G

V

V

E

E

P

P

A

D

G

E

F

S

D

N

E

C

T

L

R

Q

R

A

S

A

L

M

E

A

S

A

G

G

R

E

R

R

E

V

T

V

I

L

D

G

K

Q

D

-

A

V

R

G

S

L

I

F

C

A

D

D

A

G

L

V

L

A

T

V

P

A

I

Q

P

I

G

G

D

Q

L

H

T

T

W

F

P

D

I

I

N

C

Q

K

K

D

N

H

L

V

S

D

G

E

V

V

V

I

A

T

V

V

T

S

D

T

A

D

E

E

V

I

A

C

E

A

A

A

M

I

R

K

Y

D

A

I

F

Y

S

D

T

D

L

T

K

R

L

S

V

I

V

T

E

E

P

P

G

A

G

G

C

A

V

L

A

A

L

V

T

-

A

A

A

G

L

I

T

K

G

K

K

Y

V

V

D

E

-

R

-

E

-

R

V

A

A

E

G

G

K

Q

T

T

V

L

A

V

I

A

V

I

L

D

S

S

G

G

G

A

N

N

V

V

D

N

binding 2-ketobutyric acid: K50 (= K52), S74 (= S76), H78 (= H80)

Sites not aligning to the query:

binding 2-ketobutyric acid: 336, 337, 338, 340, 341, 358, 448, 449

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, 96% coverage: 3:313/325 of query aligns to 7:318/340 of Q9GZT4

query
sites
Q9GZT4

V

I

S

S

L

F

A

A

D

D

I

V

Q
x
E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S
|
S

P
x
S

A
x
I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R
x
K

A
x
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-
x
P

-

D

S

A

D

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A
x
T

F

H

S

S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F
x
Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D
|
D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A

G

L

V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L
x
N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K
|
K

L

L

V

L

V

I

E

E

P

P

G

T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L

L

S
|
S

G

G

N
|
N

V

V

D

D

E13 (≠ Q9) binding Mg(2+)
S31 (= S27) binding ATP
S32 (≠ P28) binding ATP
I33 (≠ A29) binding ATP
K51 (≠ R47) binding ATP
T52 (≠ A48) binding ATP
K56 (= K52) modified: N6-(pyridoxal phosphate)lysine
P69 (vs. gap) binding Ca(2+)
T81 (≠ A74) binding Ca(2+)
N86 (= N79) binding pyridoxal 5'-phosphate
Q89 (= Q82) binding ATP
Y121 (≠ F114) binding ATP
D178 (= D175) binding Mg(2+)
G185 (= G182) binding pyridoxal 5'-phosphate
G186 (= G183) binding pyridoxal 5'-phosphate
G187 (= G184) binding pyridoxal 5'-phosphate
G188 (= G185) binding pyridoxal 5'-phosphate
M189 (≠ L186) binding pyridoxal 5'-phosphate
E210 (= E207) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ F211) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ E213) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L245) binding Ca(2+); binding Mg(2+)
K279 (= K277) binding ATP
S313 (= S308) binding pyridoxal 5'-phosphate
N316 (= N311) binding ATP

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/322 of 7nbgAAA

query
sites
7nbgAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I
|
I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K
|
K

V

K

E

L

G

A

T
x
I

R

Q

G

A

F
x
Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L

N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G283), S310 (= S308), G311 (= G309)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (= S77), G85 (≠ A81), Q86 (= Q82), I101 (= I97), K111 (= K107), I115 (≠ T111), Y118 (≠ F114)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/323 of 7nbfAAA

query
sites
7nbfAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V
x
H

E
x
L

T
|
T

P
|
P

L

V

I
x
L

E
x
T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L
x
F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F

Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L
x
N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding magnesium ion: N244 (≠ L245)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G283), S310 (= S308), G311 (= G309)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ V20), L22 (≠ E21), T23 (= T22), P24 (= P23), L26 (≠ I25), T27 (≠ E26), F46 (≠ L45)

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)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/323 of 7nbdAAA

query
sites
7nbdAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F

Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L
x
N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F
x
W

S

E

T

R

L

M

K

K

L

L

V
x
L

V

I

E
|
E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V
|
V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ F273), L278 (≠ V279), V314 (= V312)
binding magnesium ion: N244 (≠ L245)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), E280 (= E281), T282 (≠ G283), S310 (= S308), G311 (= G309)

Sites not aligning to the query:

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/323 of 7nbcCCC

query
sites
7nbcCCC

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A
x
T

F
x
H

S

S

S
|
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F

Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V
|
V

P
x
H

S
x
P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L

N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding biphenyl-4-ylacetic acid: T78 (≠ A74), H79 (≠ F75), H84 (= H80), V148 (= V144), H149 (≠ P145), P150 (≠ S146)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G283), S310 (= S308), G311 (= G309)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/323 of 7nbcAAA

query
sites
7nbcAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F

Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L
x
N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E

E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding magnesium ion: N244 (≠ L245)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N83 (= N79), G182 (= G182), G183 (= G183), G184 (= G184), G185 (= G185), M186 (≠ L186), G236 (≠ A236), V237 (≠ L237), T282 (≠ G283), S310 (= S308), G311 (= G309)

Sites not aligning to the query:

binding magnesium ion: 3

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:315/320 of 7nbhAAA

query
sites
7nbhAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

-

V

-

P

-

D

S

A

D

L

E

E

E

R

K

K

A

P

R

K

G

A

V

V

A

T

F

H

S

S

S
|
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K
|
K

V

K

E

L

G

A

T
x
I

R

Q

G

A

F
x
Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G

G

L

M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D
|
D

A
x
G

L

V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L

N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E

E

P
|
P

G

T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G

G

N
|
N

V
|
V

D
|
D

active site: K53 (= K52), S81 (= S77), E207 (= E207), A211 (≠ F211), D213 (≠ E213), G236 (≠ A236), L309 (= L307), S310 (= S308)
binding calcium ion: E207 (= E207), A211 (≠ F211), D213 (≠ E213)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (= S77), G85 (≠ A81), Q86 (= Q82), K111 (= K107), I115 (≠ T111), Y118 (≠ F114), D235 (= D235), P281 (= P282), N313 (= N311), V314 (= V312), D315 (= D313)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:310/310 of 7nbgDDD

query
sites
7nbgDDD

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

S

V

D

-

E

-

E

R

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I
|
I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F
x
Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R

R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L
x
N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E
|
E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K53 (= K52), S76 (= S77), E202 (= E207), A206 (≠ F211), D208 (≠ E213), G231 (≠ A236), L304 (= L307), S305 (= S308)
binding calcium ion: E202 (= E207), A206 (≠ F211), D208 (≠ E213)
binding magnesium ion: N239 (≠ L245)
binding ortho-xylene: S76 (= S77), Q81 (= Q82), I96 (= I97), Y113 (≠ F114)
binding pyridoxal-5'-phosphate: F52 (= F51), K53 (= K52), N78 (= N79), G177 (= G182), G178 (= G183), G179 (= G184), G180 (= G185), M181 (≠ L186), G231 (≠ A236), V232 (≠ L237), E275 (= E281), T277 (≠ G283), S305 (= S308), G306 (= G309)

Sites not aligning to the query:

binding magnesium ion: 3

6zspAAA serine racemase bound to atp and malonate. (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 4:308/320 of 6zspAAA

query
sites
6zspAAA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S
|
S

P
x
S

A
x
I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R
x
K

A
x
T

G

G

A

S

F

F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

S

-

D

-

E

-

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F
x
Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R
|
R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G

G

L

M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L

V

L

K

T
x
S

P

S

I

I

P

-

G

G

D

L

L

N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S
x
E

T
x
R

L

M

K
|
K

L

L

V

L

V

I

E

E

P

P

G

T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G

G

N
|
N

V

V

D

D

active site: K53 (= K52), S74 (= S77), E200 (= E207), A204 (≠ F211), D206 (≠ E213), G229 (≠ A236), L302 (= L307), S303 (= S308)
binding adenosine-5'-triphosphate: S28 (= S27), S29 (≠ P28), I30 (≠ A29), K48 (≠ R47), T49 (≠ A48), Q79 (= Q82), Y111 (≠ F114), E266 (≠ S274), R267 (≠ T275), K269 (= K277), N306 (= N311)
binding magnesium ion: E200 (= E207), A204 (≠ F211), D206 (≠ E213)
binding malonate ion: K53 (= K52), S73 (= S76), S74 (= S77), N76 (= N79), H77 (= H80), R125 (= R128), G229 (≠ A236), S232 (≠ T239)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
35% identity, 96% coverage: 3:313/325 of query aligns to 5:311/322 of 3l6bA

query
sites
3l6bA

V

I

S

S

L

F

A

A

D

D

I

V

Q

E

A

K

A

A

A

H

V

I

R

N

L

I

K

R

G

D

S

S

A

I

V

H

E

L

T

T

P

P

L

V

I

L

E

T

S

S

P

S

A

I

L

L

N

N

D

Q

R

L

L

T

G

G

G

R

R

N

I

L

F

F

L

F

K

K

P

C

E

E

T

L

L

F

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

I

R

R

G

G

A

A

Y

L

N

N

R

A

L

V

S

R

Q

S

L

L

S

V

D

-

E

-

E

R

K

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

G

A

V

L

A

T

L

Y

A

A

R

K

L

L

L

E

G

G

V

I

P

P

A

A

L

Y

I

I

V

V

M

V

P

P

S

Q

D

T

S

A

P

P

S

D

V

C

K

K

V

K

E

L

G

A

T

I

R

Q

G

A

F

Y

G

G

A

A

D

S

I

I

R

V

F

Y

Y

C

D

E

R

P

F

S

T

D

E

E

D

S

R
|
R

V

E

A

N

I

V

A

A

D

K

Q

R

I

V

A

T

A

E

E

E

R

T

G

E

C

G

V

I

V

M

V

V

P

H

S

P

Y

N

D

Q

D

E

P

P

H

A

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

A

N

Q

Q

A

V

A

-

Q

-

G

-

A

P

T

L

L

V

D

D

R

A

L

L

I

V

C

V

C

P

V

V

G
|
G

L
x
M

I

L

A

A

G

G

T

I

S

A

T

I

A

T

V

V

K

K

A

A

L

L

S

K

P

P

A

S

T

V

E

K

I

V

W

Y

G

A

V

A

E
|
E

P

P

A

S

G

N

F
x
A

D

D

E
x
D

T

C

R

Y

R

Q

S

S

L

K

E

L

S

K

G

G

R

K

R

L

E

M

T

P

I

N

D

L

K

Y

D

P

A

P

R

E

S

T

I

I

C

A

D

D

A
x
G

L
x
V

L

K

T

S

P

S

I

I

P

-

G

G

D

L

L

N

T

T

W

W

P

P

I

I

N

I

Q

R

K

D

N

L

L

V

S

D

G

D

V

I

V

F

A

T

V

V

T

T

D

E

A

D

E

E

V

I

A

K

E

C

A

A

M

T

R

Q

Y

L

A

V

F

W

S

E

T

R

L

M

K

K

L

L

V

L

V

I

E
|
E

P

P

G
x
T

G

A

C

G

V

V

A

G

L

V

T

A

A

A

A

V

L

L

T

S

G

Q

K

H

V

F

D

Q

V

T

A

V

G

S

-

P

-

E

-

V

K

K

T

N

V

I

A

C

I

I

V

V

L
|
L

S
|
S

G
|
G

G

G

N

N

V

V

D

D

active site: K54 (= K52), S77 (= S77), E203 (= E207), A207 (≠ F211), D209 (≠ E213), G232 (≠ A236), T278 (≠ G283), L305 (= L307), S306 (= S308)
binding malonate ion: K54 (= K52), S76 (= S76), S77 (= S77), N79 (= N79), H80 (= H80), R128 (= R128), G232 (≠ A236)
binding manganese (ii) ion: E203 (= E207), A207 (≠ F211), D209 (≠ E213)
binding pyridoxal-5'-phosphate: F53 (= F51), K54 (= K52), N79 (= N79), G178 (= G182), G179 (= G183), G180 (= G184), G181 (= G185), M182 (≠ L186), V233 (≠ L237), E276 (= E281), T278 (≠ G283), S306 (= S308), G307 (= G309)

1ve5A Crystal structure of t.Th. Hb8 threonine deaminase
43% identity, 95% coverage: 4:313/325 of query aligns to 2:305/308 of 1ve5A

query
sites
1ve5A

S

S

L

L

A

Q

D

D

I

L

Q

Y

A

A

A

F

V

R

R

R

L

I

K

A

G

P

S

Y

A

T

V

H

E

R

T

T

P

P

L

L

I

L

E

T

S

S

P

R

A

L

L

L

N

D

D

G

R

L

L

L

G

G

G

K

R

R

I

L

F

L

L

L

K

K

P

A

E

E

T

H

L

L

Q

Q

R

K

A

T

G

G

A

S

F
|
F

K
|
K

F

A

R

R

G

G

A

A

Y

L

N
x
S

R

K

L

A

S

L

Q

A

L

L

S

-

D

-

E

-

E

E

K

N

A

P

R

K

G

G

V

L

A

A

F

V

S

S

S
|
S

G

G

N
|
N

H

H

A

A

Q

Q

G

G

V

V

A

A

L

Y

A

A

R

Q

L

V

L

L

G

G

V

V

P

K

A

A

L

L

I

V

V

V

M

M

P

P

S

E

D

D

S

P

P

-

S

-

V

Y

K

K

V

K

E

A

G

C

T

A

R

R

G

A

F

Y

G

G

A

A

D

E

I

V

R

V

F

D

Y

R

D

G

R

V

F

T

T

A

E

K

D

N

R

R

V

E

A

E

I

V

A

A

D

R

Q

A

I

L

A

Q

A

E

E

E

R

T

G

G

C

Y

V

A

V

L

V

I

P

H

S

P

Y

F

D

D

P

P

H

L

I

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

A

G

G

L

L

E

E

I

L

V

L

A

A

Q

Q

A

A

A

G

A

R

Q

M

G

G

A

V

T

F

L

P

D

G

R

A

L

V

I

L

C

A

C

P

V

V

G
|
G

L

L

I

L

A

A

G

G

T

L

S

A

T

T

A

A

V

V

K

K

A

A

L

L

S

S

P

P

A

T

T

T

E

L

I

V

W

L

G

G

V

V

E
|
E

P

P

A

E

G

A

F
x
A

D

D

E
x
D

T

A

R

K

R

R

S

S

L

L

E

E

S

A

G

G

R

R

R

I

E

L

T

R

I

L

D

E

K

A

D

P

A

P

R

R

S

T

I

R

C

A

D

D

A
x
G

L

V

L

R

T

T

P

L

I

S

P

L

G

G

D

E

L

R

T

T

W

F

P

P

I

I

N

L

Q

R

K

E

N

R

L

V

S

D

G

G

V

I

V

L

A

T

V

V

T

S

D

E

A

E

E

A

V

L

A

L

E

E

A

A

M

E

R

R

Y

L

A

L

F

F

S

T

T

R

L

T

K

K

L

Q

V

V

E
|
E

P

P

G
x
T

G

G

C

A

V

L

A

P

L

L

T

A

A

A

A

V

L

L

T

E

G

H

K

G

V

A

D

R

V

L

A

P

G

-

K

Q

T

T

V

L

A

A

I

L

V

L

L
|
L

S
|
S

G
|
G

G

G

N

N

V

R

D

D

active site: K50 (= K52), S56 (≠ N58), S72 (= S77), E200 (= E207), A204 (≠ F211), D206 (≠ E213), G229 (≠ A236), L299 (= L307), S300 (= S308)
binding calcium ion: E200 (= E207), A204 (≠ F211), D206 (≠ E213)
binding pyridoxal-5'-phosphate: F49 (= F51), K50 (= K52), N74 (= N79), G175 (= G182), G176 (= G183), G177 (= G184), G178 (= G185), E274 (= E281), T276 (≠ G283), S300 (= S308), G301 (= G309)

Query Sequence

>CCNA_03203 FitnessBrowser__Caulo:CCNA_03203
MTVSLADIQAAAVRLKGSAVETPLIESPALNDRLGGRIFLKPETLQRAGAFKFRGAYNRL
SQLSDEEKARGVVAFSSGNHAQGVALAARLLGVPALIVMPSDSPSVKVEGTRGFGADIRF
YDRFTEDRVAIADQIAAERGCVVVPSYDDPHIIAGQGTVGLEIVAQAAAQGATLDRLICC
VGGGGLIAGTSTAVKALSPATEIWGVEPAGFDETRRSLESGRRETIDKDARSICDALLTP
IPGDLTWPINQKNLSGVVAVTDAEVAEAMRYAFSTLKLVVEPGGCVALTAALTGKVDVAG
KTVAIVLSGGNVDPGLFAQVLGGQI

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