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)
43% identity, 74% coverage: 21:336/427 of query aligns to 2:321/326 of 2gn2A

query
sites
2gn2A

T

T

A

Y

A

D

L

L

P

P

V

V

S

A

L

I

D

E

D

D

I

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K

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F

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E

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N

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x
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T

A
x
G

S

S

F

F

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E

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A

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F

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N

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K

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E

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K

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G

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x
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I

active site: K56 (= K75), A81 (= A100), Q207 (≠ E226), V211 (≠ A229), G213 (≠ A231), G235 (= G252), I308 (≠ L323), S309 (≠ C324)
binding cytidine-5'-monophosphate: R51 (≠ F70), T52 (= T71), G53 (≠ A72), A114 (≠ H133), D117 (≠ N136), Y118 (≠ F137), N312 (= N327)

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)
42% identity, 73% coverage: 27:337/427 of query aligns to 5:317/319 of A4F2N8

query
sites
A4F2N8

S

S

L

Y

D

H

D

D

I

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I

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K

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A

E

E

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K

E

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A

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K53 (= K75) mutation to A: Loss of enzymatic activity.

Q7XSN8 Serine racemase; D-serine dehydratase; D-serine ammonia-lyase; L-serine dehydratase; L-serine ammonia-lyase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Oryza sativa subsp. japonica (Rice) (see paper)
34% identity, 73% coverage: 28:340/427 of query aligns to 21:339/339 of Q7XSN8

query
sites
Q7XSN8

L

I

D

H

D

S

I

I

R

R

A

E

A

A

A

Q

E

A

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N

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L

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T

A

A

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F

F

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K

E

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R

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G

A

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-

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x
E

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G

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Q

R

E219 (vs. gap) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ V227) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

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)
37% identity, 72% coverage: 21:329/427 of query aligns to 2:318/340 of Q9GZT4

query
sites
Q9GZT4

T

C

A

A

A

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L

Y

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V

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F

D

A

D

D

I

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x
E

A

K

A

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A

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x
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x
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T

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G

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N

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K

F

C

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E

N

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L

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Q

F
x
K

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T

A

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S

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E

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G

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A

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N

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E
x
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D

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A

-

L

E

E

E

R

R

K

R

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R

K

G

A

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V

A
x
T

M

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A

S

G

G

N
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N

H

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A

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Q

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A

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A

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A
x
D

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K

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L

L

C
x
S

G

G

N
|
N

I

V

D

D

E13 (≠ R32) binding Mg(2+)
S31 (= S50) binding ATP
S32 (≠ R51) binding ATP
I33 (≠ T52) binding ATP
K51 (≠ F70) binding ATP
T52 (= T71) binding ATP
K56 (= K75) modified: N6-(pyridoxal phosphate)lysine
P69 (≠ E88) binding Ca(2+)
T81 (≠ A97) binding Ca(2+)
N86 (= N102) binding pyridoxal 5'-phosphate
Q89 (= Q105) binding ATP
Y121 (≠ F137) binding ATP
D178 (≠ E194) binding Mg(2+)
G185 (= G201) binding pyridoxal 5'-phosphate
G186 (= G202) binding pyridoxal 5'-phosphate
G187 (= G203) binding pyridoxal 5'-phosphate
G188 (= G204) binding pyridoxal 5'-phosphate
M189 (≠ L205) binding pyridoxal 5'-phosphate
E210 (= E226) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ Y230) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ A232) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (≠ L261) binding Ca(2+); binding Mg(2+)
K279 (= K293) binding ATP
S313 (≠ C324) binding pyridoxal 5'-phosphate
N316 (= N327) binding ATP

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)
36% identity, 74% coverage: 20:337/427 of query aligns to 3:321/323 of O59791

query
sites
O59791

D

D

T

N

A

L

A

V

L

L

P

P

V

-

S

T

L

Y

D

D

I

V

R

A

A

S

A

A

A

S

E

E

A

R

L

I

R

K

G

K

Q

F

V

A

V

N

E

K

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

T

L

V

S

N

Q

K

I

E

T

F

G

V

A

A

E

E

I

V

W

F

V

F

K

K

F

C

E

E

N

N

L

F

Q

Q

F

K

T

M

A

G

S

A

F

F

K
|
K

E

F

R

R

G

G

A

A

F

L

N

N

K

A

L

L

R

S

T

Q

L

L

T

N

E

E

E

A

E

Q

R

R

R

K

R

A

G

G

V

V

V

L

A

T

M

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

Y

L

H

S

A

A

G

K

R

I

L

L

G

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

E

L

G

D

T

A

P

P

F

E

V

A

K

K

V

V

E

A

H

A

T

T

E

K

N

G

F

Y

G

G

A

G

R

Q

V

V

V

I

L

M

K

Y

G

D

A

R

N

Y

L

K

G

D

E

D

S

R

Q

E

I

K

E

M

A

A

E

K

R

E

L

I

V

S

R

E

E

R

E

E

G

G

L

L

V

T

L

I

V

I

H

P

P

P

Y

Y

D

D

D

H

A

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

L

K

E

E

M

L

L

F

A

E

A

V

P

G

D

P

L

L

E

D

V

A

L

L

V

F

V

V

P

C

V

L

G
|
G

L
|
L

I

L

S

S

G

G

I

S

A

A

T

L

A

A

K

R

A

H

V

F

K

A

P

P

D

N

I

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

V

P

E

E

A

A

Y
x
G

A

N

A
x
D

V

G

A

Q

Q

Q

A

S

L

F

R

R

-

K

G

G

E

S

P

I

P

V

H

H

V

I

G

D

G

T

-

P

D

K

T

T

I

I

A

A

E

D

G

G

I

A

A

Q

V

T

K

Q

N

H

V

L

G

G

R

N

L

Y

T

T

L

F

Q

S

I

I

R

K

A

E

L

K

V

V

D

D

E

D

V

I

M

L

L

T

V

V

P

S

D

D

A

E

E

E

V

L

E

I

R

D

A

C

V

L

A

K

L

F

F

Y

L

A

N

A

I

R

E

M

K

K

T

I

V

V

A

V

E

E

G

P

A

T

G

G

A

C

A

L

G

S

L

F

A

A

V

A

L

R

N

A

H

M

P

K

E

E

R

K

F

L

Q

K

G

N

R

K

K

R

V

I

G

G

L

I

V

I

L

I

C
x
S

G

G

N

N

I

V

D

D

S

I

R

E

L

R

L

Y

A

A

Q

H

V

F

I

L

K57 (= K75) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ A100) 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 (= N102) binding pyridoxal 5'-phosphate
G183 (= G201) binding pyridoxal 5'-phosphate
G184 (= G202) binding pyridoxal 5'-phosphate
G185 (= G203) binding pyridoxal 5'-phosphate
G186 (= G204) binding pyridoxal 5'-phosphate
L187 (= L205) binding pyridoxal 5'-phosphate
E208 (= E226) binding Mg(2+)
G212 (≠ Y230) binding Mg(2+)
D214 (≠ A232) binding Mg(2+)
S308 (≠ C324) binding pyridoxal 5'-phosphate

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/323 of 7nbfAAA

query
sites
7nbfAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V
x
H

E
x
L

T
|
T

P
|
P

C

V

I
x
L

P
x
T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L
x
F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F

Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L
x
N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding magnesium ion: N244 (≠ L261)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N83 (= N102), G182 (= G201), G183 (= G202), G184 (= G203), G185 (= G204), M186 (≠ L205), G236 (= G252), V237 (≠ I253), T282 (≠ A299), S310 (≠ C324), G311 (= G325)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ V43), L22 (≠ E44), T23 (= T45), P24 (= P46), L26 (≠ I48), T27 (≠ P49), F46 (≠ L68)

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)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/323 of 7nbdAAA

query
sites
7nbdAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F

Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L
x
N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L
x
W

N

E

I

R

E

M

K

K

T

L

V
x
L

A

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I
x
V

D

D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ L289), L278 (≠ V295), V314 (≠ I328)
binding magnesium ion: N244 (≠ L261)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N83 (= N102), G182 (= G201), G183 (= G202), G184 (= G203), G185 (= G204), M186 (≠ L205), G236 (= G252), V237 (≠ I253), E280 (= E297), T282 (≠ A299), S310 (≠ C324), G311 (= G325)

Sites not aligning to the query:

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/323 of 7nbcCCC

query
sites
7nbcCCC

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A
x
T

M
x
H

S

S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F

Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V
|
V

H
|
H

P
|
P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L

N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding biphenyl-4-ylacetic acid: T78 (≠ A97), H79 (≠ M98), H84 (= H103), V148 (= V167), H149 (= H168), P150 (= P169)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N83 (= N102), G182 (= G201), G183 (= G202), G184 (= G203), G185 (= G204), M186 (≠ L205), G236 (= G252), V237 (≠ I253), T282 (≠ A299), S310 (≠ C324), G311 (= G325)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/323 of 7nbcAAA

query
sites
7nbcAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q

Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F

Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L
x
N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding magnesium ion: N244 (≠ L261)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N83 (= N102), G182 (= G201), G183 (= G202), G184 (= G203), G185 (= G204), M186 (≠ L205), G236 (= G252), V237 (≠ I253), T282 (≠ A299), S310 (≠ C324), G311 (= G325)

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)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/320 of 7nbhAAA

query
sites
7nbhAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F

F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N

N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K
|
K

V

K

E

L

H

A

T
x
I

E

Q

N

A

F
x
Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G

G

L

M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E
x
D

G
|
G

I

V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L

N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G
x
P

A

T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G

G

N
|
N

I
x
V

D
|
D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ A100), G85 (≠ A104), Q86 (= Q105), K111 (= K130), I115 (≠ T134), Y118 (≠ F137), D235 (≠ E251), P281 (≠ G298), N313 (= N327), V314 (≠ I328), D315 (= D329)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:315/322 of 7nbgAAA

query
sites
7nbgAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

P

-

D

-

A

-

L

E

E

E

R

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N
|
N

H

H

A
x
G

Q
|
Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K
|
K

V

K

E

L

H

A

T
x
I

E

Q

N

A

F
x
Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L

N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E

E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K75), S81 (≠ A100), E207 (= E226), A211 (≠ Y230), D213 (≠ A232), G236 (= G252), L309 (= L323), S310 (≠ C324)
binding calcium ion: E207 (= E226), A211 (≠ Y230), D213 (≠ A232)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N83 (= N102), G182 (= G201), G183 (= G202), G184 (= G203), G185 (= G204), M186 (≠ L205), G236 (= G252), V237 (≠ I253), T282 (≠ A299), S310 (≠ C324), G311 (= G325)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ A100), G85 (≠ A104), Q86 (= Q105), I101 (= I120), K111 (= K130), I115 (≠ T134), Y118 (≠ F137)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
37% identity, 72% coverage: 22:329/427 of query aligns to 1:311/322 of 3l6bA

query
sites
3l6bA

A

A

A

Q

L

Y

P

D

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

R

E

-

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q

Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F

Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S
x
R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L

N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K54 (= K75), S77 (≠ A100), E203 (= E226), A207 (≠ Y230), D209 (≠ A232), G232 (= G252), T278 (≠ A299), L305 (= L323), S306 (≠ C324)
binding malonate ion: K54 (= K75), S76 (= S99), S77 (≠ A100), N79 (= N102), H80 (= H103), R128 (≠ S151), G232 (= G252)
binding manganese (ii) ion: E203 (= E226), A207 (≠ Y230), D209 (≠ A232)
binding pyridoxal-5'-phosphate: F53 (= F74), K54 (= K75), N79 (= N102), G178 (= G201), G179 (= G202), G180 (= G203), G181 (= G204), M182 (≠ L205), V233 (≠ I253), E276 (= E297), T278 (≠ A299), S306 (≠ C324), G307 (= G325)

1wtcA Crystal structure of s.Pombe serine racemase complex with amppcp (see paper)
36% identity, 74% coverage: 24:337/427 of query aligns to 2:316/318 of 1wtcA

query
sites
1wtcA

L

L

P

P

V

-

S

T

L

Y

D

D

I

V

R

A

A

S

A

A

A

S

E

E

A

R

L

I

R

K

G

K

Q

F

V

A

V
x
N

E

K

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

T

L

V

S

N

Q

K

I

E

T

F

G

V

A

A

E

E

I

V

W

F

V

F

K

K

F

C

E

E

N

N

L

F

Q

Q

F
x
K

T
x
M

A

G

S

A

F
|
F

K
|
K

E

F

R

R

G

G

A

A

F

L

N

N

K

A

L

L

R

S

T

Q

L

L

T

N

E

E

E

A

E

Q

R

R

R

K

R

A

G

G

V

V

V

L

A

T

M

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

Y

L

H

S

A

A

G

K

R

I

L

L

G

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

E

L

G

D

T

A

P

P

F

E

V

A

K

K

V

V

E
x
A

H
x
A

T

T

E

K

N

G

F
x
Y

G

G

A

G

R

Q

V

V

V

I

L

M

K

Y

G

D

A

R

N

Y

L

K

G

D

E

D

S

R

Q

E

I

K

E

M

A

A

E

K

R

E

L

I

V

S

R

E

E

R

E

E

G

G

L

L

V

T

L

I

V

I

H

P

P

P

Y

Y

D

D

D

H

A

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

L

K

E

E

M

L

L

F

A

E

A

V

P

G

D

P

L

L

E

D

V

A

L

L

V

F

V

V

P

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

T

L

A

A

K

R

A

H

V

F

K

A

P

P

D

N

I

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

V

P

E

E

A

A

Y
x
G

A

N

A
x
D

V

G

A

Q

Q

Q

A

S

L

F

R

R

-

K

G

G

E

S

P

I

P

V

H

H

V

I

G

D

G

T

-

P

D

K

T

T

I

I

A

A

E

D

G
|
G

I

A

A

Q

V

T

K

Q

N

H

V

L

G

G

R

N

L

Y

T

T

L

F

Q

S

I

I

R

K

A

E

L

K

V

V

D

D

E

D

V

I

M

L

L

T

V

V

P

S

D

D

A

E

E

E

V

L

E

I

R

D

A

C

V

L

A

K

L

F

F

Y

L

A

N

A

I

R

E

M

K

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

G

S

L

F

A

A

V

A

L

R

N

A

H

M

P

K

E

E

R

K

F

L

Q

K

G

N

R

K

K

R

V

I

G

G

L

I

V

I

L
x
I

C
x
S

G

G

N

N

I

V

D

D

S

I

R

E

L

R

L

Y

A

A

Q

H

V

F

I

L

active site: K52 (= K75), S77 (≠ A100), E203 (= E226), G207 (≠ Y230), D209 (≠ A232), G231 (= G252), I302 (≠ L323), S303 (≠ C324)
binding phosphomethylphosphonic acid adenylate ester: N20 (≠ V43), K47 (≠ F70), M48 (≠ T71), A109 (≠ E132), A110 (≠ H133), Y114 (≠ F137)
binding magnesium ion: E203 (= E226), G207 (≠ Y230), D209 (≠ A232)
binding pyridoxal-5'-phosphate: F51 (= F74), K52 (= K75), N79 (= N102), G178 (= G201), G179 (= G202), G180 (= G203), G181 (= G204), G231 (= G252), E276 (= E297), T278 (≠ A299), S303 (≠ C324)

1v71A Crystal structure of s.Pombe serine racemase
36% identity, 74% coverage: 24:337/427 of query aligns to 2:316/318 of 1v71A

query
sites
1v71A

L

L

P

P

V

-

S

T

L

Y

D

D

I

V

R

A

A

S

A

A

A

S

E

E

A

R

L

I

R

K

G

K

Q

F

V

A

V

N

E

K

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

T

L

V

S

N

Q

K

I

E

T

F

G

V

A

A

E

E

I

V

W

F

V

F

K

K

F

C

E

E

N

N

L

F

Q

Q

F

K

T

M

A

G

S

A

F
|
F

K
|
K

E

F

R

R

G

G

A

A

F

L

N

N

K

A

L

L

R

S

T

Q

L

L

T

N

E

E

E

A

E

Q

R

R

R

K

R

A

G

G

V

V

V

L

A

T

M

F

S

S

A
x
S

G

G

N
|
N

H

H

A

A

Q

Q

G

A

V

I

A

A

Y

L

H

S

A

A

G

K

R

I

L

L

G

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

E

L

G

D

T

A

P

P

F

E

V

A

K

K

V

V

E

A

H

A

T

T

E

K

N

G

F

Y

G

G

A

G

R

Q

V

V

V

I

L

M

K

Y

G

D

A

R

N

Y

L

K

G

D

E

D

S

R

Q

E

I

K

E

M

A

A

E

K

R

E

L

I

V

S

R

E

E

R

E

E

G

G

L

L

V

T

L

I

V

I

H

P

P

P

Y

Y

D

D

D

H

A

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

L

K

E

E

M

L

L

F

A

E

A

V

P

G

D

P

L

L

E

D

V

A

L

L

V

F

V

V

P

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

T

L

A

A

K

R

A

H

V

F

K

A

P

P

D

N

I

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

V

P

E

E

A

A

Y
x
G

A

N

A
x
D

V

G

A

Q

Q

Q

A

S

L

F

R

R

-

K

G

G

E

S

P

I

P

V

H

H

V

I

G

D

G

T

-

P

D

K

T

T

I

I

A

A

E

D

G
|
G

I

A

A

Q

V

T

K

Q

N

H

V

L

G

G

R

N

L

Y

T

T

L

F

Q

S

I

I

R

K

A

E

L

K

V

V

D

D

E

D

V

I

M

L

L

T

V

V

P

S

D

D

A

E

E

E

V

L

E

I

R

D

A

C

V

L

A

K

L

F

F

Y

L

A

N

A

I

R

E

M

K

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

G

S

L

F

A

A

V

A

L

R

N

A

H

M

P

K

E

E

R

K

F

L

Q

K

G

N

R

K

K

R

V

I

G

G

L

I

V

I

L
x
I

C
x
S

G
|
G

G

G

N

N

I

V

D

D

S

I

R

E

L

R

L

Y

A

A

Q

H

V

F

I

L

active site: K52 (= K75), S77 (≠ A100), E203 (= E226), G207 (≠ Y230), D209 (≠ A232), G231 (= G252), I302 (≠ L323), S303 (≠ C324)
binding magnesium ion: E203 (= E226), G207 (≠ Y230), D209 (≠ A232)
binding pyridoxal-5'-phosphate: F51 (= F74), K52 (= K75), N79 (= N102), G178 (= G201), G179 (= G202), G180 (= G203), G181 (= G204), G231 (= G252), E276 (= E297), T278 (≠ A299), S303 (≠ C324), G304 (= G325)

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:310/310 of 7nbgDDD

query
sites
7nbgDDD

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F

K

T

T

A

G

S

S

F
|
F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

V

E

R

E

-

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S

S

A
x
S

G

G

N
|
N

H

H

A

G

Q
|
Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I
|
I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F
x
Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S

R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

D

Q

D

E

A

P

E

A

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

I

A

A

L

L

E

E

M

V

L

L

A

N

A

Q

A

V

P

P

D

L

L

V

E

D

V

A

L

L

V

V

P

P

V

V

G
|
G

L
x
M

I

L

S

A

G

G

I

I

A

A

T

I

A

T

A

V

K

K

A

A

V

L

K

K

P

P

D

S

I

V

E

K

V

V

V

Y

G

A

V

A

E
|
E

V

P

E

S

A

N

Y
x
A

A

D

A
x
D

V

C

A

Y

Q

Q

A

S

-

K

L

L

R

K

G

G

E

K

-

L

-

M

P

P

P

N

H

L

V

Y

G

P

D

E

T

T

I

I

A

A

E

D

G
|
G

I
x
V

A

K

V

-

K

S

N

S

V

I

G

G

R

L

L
x
N

T

T

L

W

Q

P

I

I

R

R

A

D

L

L

V

V

D

D

E

D

V

I

M

F

L

T

V

V

P

T

D

E

A

D

E

E

V

I

E

K

R

C

A

A

V

T

A

Q

L

L

F

V

L

W

N

E

I

R

E

M

K

K

T

L

V

L

A

I

E
|
E

G

P

A
x
T

G

A

A

G

A

V

G

G

L

V

A

A

V

V

L

L

N

S

H

-

P

-

E

Q

R

H

F

F

Q

Q

G

T

-

V

-

S

-

P

-

E

-

V

R

K

K

N

V

I

G

C

L

I

V

V

L
|
L

C
x
S

G
|
G

G

G

N

N

I

V

D

D

active site: K53 (= K75), S76 (≠ A100), E202 (= E226), A206 (≠ Y230), D208 (≠ A232), G231 (= G252), L304 (= L323), S305 (≠ C324)
binding calcium ion: E202 (= E226), A206 (≠ Y230), D208 (≠ A232)
binding magnesium ion: N239 (≠ L261)
binding ortho-xylene: S76 (≠ A100), Q81 (= Q105), I96 (= I120), Y113 (≠ F137)
binding pyridoxal-5'-phosphate: F52 (= F74), K53 (= K75), N78 (= N102), G177 (= G201), G178 (= G202), G179 (= G203), G180 (= G204), M181 (≠ L205), G231 (= G252), V232 (≠ I253), E275 (= E297), T277 (≠ A299), S305 (≠ C324), G306 (= G325)

Sites not aligning to the query:

binding magnesium ion: 3

1tdjA Threonine deaminase (biosynthetic) from e. Coli (see paper)
36% identity, 91% coverage: 38:424/427 of query aligns to 17:406/494 of 1tdjA

query
sites
1tdjA

L

L

R

R

G

A

Q

P

V

V

V

Y

E

E

-

A

-

Q

-

V

T

T

P

P

C

L

I

Q

P

K

S

M

R

E

T

K

L

L

S

S

Q

S

I

R

T

L

G

D

A

N

E

V

I

I

W

L

V

V

K

K

F

R

E

E

N

D

L

R

Q

Q

F

P

T

V

A

H

S

S

F
|
F

K
|
K

E

L

R

R

G

G

A

A

F

Y

N

A

K

M

L

M

R

A

T

G

L

L

T

T

E

E

E

Q

R

K

R

A

R

H

G

G

V

V

V

I

A

T

M

A

S

S

A
|
A

G

G

N
|
N

H

H

A

A

Q

Q

G

G

V

V

A

A

Y

F

H

S

A

S

G

A

R

R

L

L

G

G

V

V

P

K

A

A

T

L

I

I

V

V

M

M

P

P

E

T

G

A

T

T

P

A

F

D

V

I

K

K

V

V

E

D

H

A

T

V

E

R

N

G

F

F

G

G

A

G

R

E

V

V

V

L

L

L

K

H

G

G

A

A

N

N

L

F

G

D

E

E

S

A

Q

K

I

A

E

K

A

A

E

I

R

E

L

L

V

S

R

Q

E

Q

G

G

L

F

V

T

L

W

V

V

H

P

P

P

Y

F

D

D

D

H

A

P

E

M

V

V

I

I

A

A

G

G

Q

Q

G

G

T

T

V

L

A

A

L

L

E

E

M

L

L

L

A

Q

A

D

P

A

D

H

L

L

E

D

V

R

L

V

V

F

V

V

P

P

V

V

G
|
G

L

L

I

A

S

A

G

G

I

V

A

A

T

V

A

L

A

I

K

K

A

Q

V

L

K

M

P

P

D

Q

I

I

E

K

V

V

V

I

G

A

V

V

E
|
E

V

A

E

E

A

D

Y
x
S

A

A

A
x
C

V

L

A

K

Q

A

A

A

L

L

R

D

-

A

G

G

E

H

P

P

-

V

-

D

-

L

P

P

H

R

V

V

G

G

G

-

D

-

T

L

I

F

A

A

E

E

G
|
G

I

V

A

A

V

V

K

K

N

R

V

I

G

G

R

D

L

E

T

T

L

F

Q

R

I

L

I

C

R

Q

A

E

L

Y

V

L

D

D

E

D

V

I

M

I

L

T

V

V

P

D

D

S

A

D

E

A

V

I

E

C

R

A

A

A

V

M

A

K

L

D

F

L

L

F

N

E

I

D

E

V

K

R

T

A

V

V

A

A

E
|
E

G

P

A

S

G

G

A

A

A

L

G

A

L

L

A

A

A

G

V

M

L

K

N

K

H

Y

-

I

-

A

P

L

E

H

R

N

F

I

Q

R

G

G

R

E

K

R

V

L

G

A

L

H

V

I

L
|
L

C
x
S

G
|
G

G

A

N

N

I

V

D

N

S

F

R

H

L

G

L

L

A

R

Q

Y

V

V

I

S

M

E

R

R

Q

C

L

E

V

L

R

G

E

E

G

Q

R

R

L

E

I

A

A

L

L

L

R

A

I

V

A

T

I

I

P

P

D

E

R

E

P

K

G

G

G

S

L

F

G

L

R

K

I

F

T

C

S

Q

V

L

G

-

E

-

A

-

G

G

N

R

I

S

I

V

E

T

A

E

M

F

H

N

Q

Y

R

R

L

F

F

-

T

-

A

A

T

D

V

A

K

K

S

N

T

A

D

C

I

I

D

F

L

V

T

G

I

V

E

R

-

L

C

S

R

R

S

G

A

L

R

E

H

E

A

R

A

K

K

E

V

I

V

L

Q

Q

A

M

L

L

R

N

D

D

A

G

G

G

F

Y

G

S

V

V

K

V

I

D

L

L

T

S

active site: K58 (= K75), A83 (= A100), E209 (= E226), S213 (≠ Y230), C215 (≠ A232), G237 (= G252), L310 (= L323), S311 (≠ C324)
binding pyridoxal-5'-phosphate: F57 (= F74), K58 (= K75), N85 (= N102), G184 (= G201), G185 (= G202), G186 (= G203), G187 (= G204), G237 (= G252), E282 (= E297), S311 (≠ C324), G312 (= G325)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
36% identity, 74% coverage: 24:337/427 of query aligns to 3:317/319 of 2zr8A

query
sites
2zr8A

L

L

P

P

V

-

S

T

L

Y

D

D

I

V

R

A

A

S

A

A

A

S

E

E

A

R

L

I

R

K

G

K

Q

F

V

A

V

N

E

K

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

T

L

V

S

N

Q

K

I

E

T

F

G

V

A

A

E

E

I

V

W

F

V

F

K

K

F

C

E

E

N

N

L

F

Q

Q

F

K

T

M

A

G

S

A

F
|
F

K
|
K

E

F

R

R

G

G

A

A

F

L

N

N

K

A

L

L

R

S

T

Q

L

L

T

N

E

E

E

A

E

Q

R

R

R

K

R

A

G

G

V

V

V

L

A

T

M

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

Y

L

H

S

A

A

G

K

R

I

L

L

G

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

E

L

G

D

T

A

P

P

F

E

V

A

K

K

V

V

E

A

H

A

T

T

E

K

N

G

F

Y

G

G

A

G

R

Q

V

V

V

I

L

M

K

Y

G

D

A

R

N

Y

L

K

G

D

E

D

S
x
R

Q

E

I

K

E

M

A

A

E

K

R

E

L

I

V

S

R

E

E

R

E

E

G

G

L

L

V

T

L

I

V

I

H

P

P
|
P

Y

Y

D

D

D

H

A

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

L

K

E

E

M

L

L

F

A

E

A

V

P

G

D

P

L

L

E

D

V

A

L

L

V

F

V

V

P

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

T

L

A

A

K

R

A

H

V

F

K

A

P

P

D

N

I

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

V

P

E

E

A

A

Y
x
G

A

N

A
x
D

V

G

A

Q

Q

Q

A

S

L

F

R

R

-

K

G

G

E

S

P

I

P

V

H

H

V

I

G

D

G

T

-

P

D

K

T

T

I

I

A

A

E
x
D

G
|
G

I
x
A

A
x
Q

V
x
T

K

Q

N

H

V

L

G

G

R

N

L

Y

T

T

L

F

Q

S

I

I

R

K

A

E

L

K

V

V

D

D

E

D

V

I

M

L

L

T

V

V

P

S

D

D

A

E

E

E

V

L

E

I

R

D

A

C

V

L

A

K

L

F

F

Y

L

A

N

A

I

R

E

M

K

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

G

S

L

F

A

A

V

A

L

R

N

A

H

M

P

K

E

E

R

K

F

L

Q

K

G

N

R

K

K

R

V

I

G

G

L

I

V

I

L
x
I

C
x
S

G

G

N

N

I

V

D

D

S

I

R

E

L

R

L

Y

A

A

Q

H

V

F

I

L

active site: K53 (= K75), S78 (≠ A100), E204 (= E226), G208 (≠ Y230), D210 (≠ A232), G232 (= G252), I303 (≠ L323), S304 (≠ C324)
binding magnesium ion: E204 (= E226), G208 (≠ Y230), D210 (≠ A232)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F74), K53 (= K75), S77 (= S99), S78 (≠ A100), N80 (= N102), H81 (= H103), P147 (= P169), G179 (= G201), G180 (= G202), G181 (= G203), G182 (= G204), G232 (= G252), E277 (= E297), T279 (≠ A299), S304 (≠ C324)
binding serine: S78 (≠ A100), R129 (≠ S151), D231 (≠ E251), G232 (= G252), A233 (≠ I253), Q234 (≠ A254), T235 (≠ V255)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
36% identity, 74% coverage: 24:337/427 of query aligns to 3:317/319 of 2zpuA

query
sites
2zpuA

L

L

P

P

V

-

S

T

L

Y

D

D

I

V

R

A

A

S

A

A

A

S

E

E

A

R

L

I

R

K

G

K

Q

F

V

A

V

N

E

K

T

T

P

P

C

V

I

L

P

T

S

S

R

S

T

T

L

V

S

N

Q

K

I

E

T

F

G

V

A

A

E

E

I

V

W

F

V

F

K

K

F

C

E

E

N

N

L

F

Q

Q

F

K

T

M

A

G

S

A

F
|
F

K
|
K

E

F

R

R

G

G

A

A

F

L

N

N

K

A

L

L

R

S

T

Q

L

L

T

N

E

E

E

A

E

Q

R

R

R

K

R

A

G

G

V

V

V

L

A

T

M

F

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

A

Q

Q

G

A

V

I

A

A

Y

L

H

S

A

A

G

K

R

I

L

L

G

G

V

I

P

P

A

A

T

K

I

I

V

I

M

M

P

P

E

L

G

D

T

A

P

P

F

E

V

A

K

K

V

V

E

A

H

A

T

T

E

K

N

G

F

Y

G

G

A

G

R

Q

V

V

V

I

L

M

K

Y

G

D

A

R

N

Y

L

K

G

D

E

D

S

R

Q

E

I

K

E

M

A

A

E

K

R

E

L

I

V

S

R

E

E

R

E

E

G

G

L

L

V

T

L

I

V

I

H

P

P
|
P

Y

Y

D

D

D

H

A

P

E

H

V

V

I

L

A

A

G

G

Q

Q

G

G

T

T

V

A

A

A

L

K

E

E

M

L

L

F

A

E

A

V

P

G

D

P

L

L

E

D

V

A

L

L

V

F

V

V

P

C

V

L

G
|
G

L

L

I

L

S

S

G

G

I

S

A

A

T

L

A

A

K

R

A

H

V

F

K

A

P

P

D

N

I

C

E

E

V

V

V

Y

G

G

V

V

E
|
E

V

P

E

E

A

A

Y
x
G

A

N

A
x
D

V

G

A

Q

Q

Q

A

S

L

F

R

R

-

K

G

G

E

S

P

I

P

V

H

H

V

I

G

D

G

T

-

P

D

K

T

T

I

I

A

A

E

D

G
|
G

I

A

A

Q

V

T

K

Q

N

H

V

L

G

G

R

N

L

Y

T

T

L

F

Q

S

I

I

R

K

A

E

L

K

V

V

D

D

E

D

V

I

M

L

L

T

V

V

P

S

D

D

A

E

E

E

V

L

E

I

R

D

A

C

V

L

A

K

L

F

F

Y

L

A

N

A

I

R

E

M

K

K

T

I

V

V

A

V

E
|
E

G

P

A
x
T

G

G

A

C

A

L

G

S

L

F

A

A

V

A

L

R

N

A

H

M

P

K

E

E

R

K

F

L

Q

K

G

N

R

K

K

R

V

I

G

G

L

I

V

I

L
x
I

C
x
S

G

G

N

N

I

V

D

D

S

I

R

E

L

R

L

Y

A

A

Q

H

V

F

I

L

active site: K53 (= K75), S78 (≠ A100), E204 (= E226), G208 (≠ Y230), D210 (≠ A232), G232 (= G252), I303 (≠ L323), S304 (≠ C324)
binding magnesium ion: E204 (= E226), G208 (≠ Y230), D210 (≠ A232)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F74), K53 (= K75), S77 (= S99), S78 (≠ A100), N80 (= N102), H81 (= H103), P147 (= P169), G179 (= G201), G180 (= G202), G181 (= G203), G182 (= G204), G232 (= G252), E277 (= E297), T279 (≠ A299), S304 (≠ C324)

6zspAAA serine racemase bound to atp and malonate. (see paper)
37% identity, 71% coverage: 26:329/427 of query aligns to 4:308/320 of 6zspAAA

query
sites
6zspAAA

V

I

S

S

L

F

D

A

D

D

I

V

R

E

A

K

A

A

A

H

E

I

A

N

L

I

R

R

G

D

Q

S

V

I

V

H

E

L

T

T

P

P

C

V

I

L

P

T

S
|
S

R
x
S

T
x
I

L

L

S

N

Q

Q

I

L

T

T

G

G

A

R

E

N

I

L

W

F

V

F

K

K

F

C

E

E

N

L

L

F

Q

Q

F
x
K

T
|
T

A

G

S

S

F

F

K
|
K

E

I

R

R

G

G

A

A

F

L

N

N

K

A

L

V

R

R

T

S

L

L

T

-

E

-

R

K

R

P

R

K

G

A

V

V

A

T

M

H

S
|
S

A
x
S

G

G

N
|
N

H
|
H

A

G

Q
|
Q

G

A

V

L

A

T

Y

Y

H

A

A

A

G

K

R

L

L

E

G

G

V

I

P

P

A

A

T

Y

I

I

V

V

M

V

P

P

E

Q

G

T

T

A

P

P

F

D

V

C

K

K

V

K

E

L

H

A

T

I

E

Q

N

A

F
x
Y

G

G

A

A

R

S

V

I

V

V

L

Y

K

C

G

E

A

P

N

S

L

D

G

E

E

S

S
x
R

Q

E

I

N

E

V

A

A

E

K

R

R

L

V

V

T

R

E

E

E

E

T

G

E

L

G

V

I

L

M

V

V

H

H

P

P

Y

N

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D

active site: K53 (= K75), S74 (≠ A100), E200 (= E226), A204 (≠ Y230), D206 (≠ A232), G229 (= G252), L302 (= L323), S303 (≠ C324)
binding adenosine-5'-triphosphate: S28 (= S50), S29 (≠ R51), I30 (≠ T52), K48 (≠ F70), T49 (= T71), Q79 (= Q105), Y111 (≠ F137), E266 (≠ N290), R267 (≠ I291), K269 (= K293), N306 (= N327)
binding magnesium ion: E200 (= E226), A204 (≠ Y230), D206 (≠ A232)
binding malonate ion: K53 (= K75), S73 (= S99), S74 (≠ A100), N76 (= N102), H77 (= H103), R125 (≠ S151), G229 (= G252), S232 (≠ K256)

Query Sequence

>WP_012568310.1 NCBI__GCF_000016185.1:WP_012568310.1
MSQRPPSSPDAAAPDAAAPDTAALPVSLDDIRAAAEALRGQVVETPCIPSRTLSQITGAE
IWVKFENLQFTASFKERGAFNKLRTLTEEERRRGVVAMSAGNHAQGVAYHAGRLGVPATI
VMPEGTPFVKVEHTENFGARVVLKGANLGESQIEAERLVREEGLVLVHPYDDAEVIAGQG
TVALEMLAAAPDLEVLVVPVGGGGLISGIATAAKAVKPDIEVVGVEVEAYAAVAQALRGE
PPHVGGDTIAEGIAVKNVGRLTLQIIRALVDEVMLVPDAEVERAVALFLNIEKTVAEGAG
AAGLAAVLNHPERFQGRKVGLVLCGGNIDSRLLAQVIMRQLVREGRLIALRIAIPDRPGG
LGRITSVVGEAGGNIIEAMHQRLFTTATVKSTDIDLTIECRSARHAAKVVQALRDAGFGV
KILTGGV

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