SitesBLAST

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, 95% coverage: 7:310/321 of query aligns to 24:329/339 of Q7XSN8

query
sites
Q7XSN8

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E219 (≠ T202) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225.
D225 (≠ R205) mutation to A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219.

2gn2A Crystal structure of tetrameric biodegradative threonine deaminase (tdcb) from salmonella typhimurium in complex with cmp at 2.5a resolution (hexagonal form) (see paper)
40% identity, 97% coverage: 2:311/321 of query aligns to 1:316/326 of 2gn2A

query
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2gn2A

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active site: K56 (= K51), A81 (≠ T76), Q207 (≠ T202), V211 (≠ G206), G213 (≠ A208), G235 (= G232), I308 (≠ L303), S309 (= S304)
binding cytidine-5'-monophosphate: R51 (≠ S46), T52 (= T47), G53 (= G48), A114 (≠ E109), D117 (≠ R112), Y118 (≠ L113), N312 (= N307)

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
34% identity, 97% coverage: 2:311/321 of query aligns to 5:313/322 of 3l6bA

query
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3l6bA

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active site: K54 (= K51), S77 (≠ T76), E203 (≠ M209), A207 (≠ I213), D209 (≠ A215), G232 (≠ S230), T278 (≠ A279), L305 (= L303), S306 (= S304)
binding malonate ion: K54 (= K51), S76 (= S75), S77 (≠ T76), N79 (= N78), H80 (= H79), R128 (≠ Q128), G232 (≠ S230)
binding manganese (ii) ion: E203 (≠ M209), A207 (≠ I213), D209 (≠ A215)
binding pyridoxal-5'-phosphate: F53 (= F50), K54 (= K51), N79 (= N78), G178 (≠ S177), G179 (= G178), G180 (= G179), G181 (= G180), M182 (≠ L181), V233 (≠ L231), E276 (= E277), T278 (≠ A279), S306 (= S304), G307 (= G305)

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)
35% identity, 98% coverage: 4:319/321 of query aligns to 7:319/319 of A4F2N8

query
sites
A4F2N8

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E

M

R

K

E

M

I

V

V

V

E

E

G

P

A

T

G

G

A

C

V

L

G

G

I

L

A

A

L

L

L

R

S

N

G

L

K

K

L

Q

A

Q

H

F

L

R

K

G

G

Q

P

R

A

V

A

G

V

I

I

I

L

V

S

T

G

G

Q

G

N

N

I

V

D

D

M

I

T

E

L

K

H

Y

R

A

K

S

I

L

V

L

N

K

G

G

K53 (= K51) mutation to A: Loss of enzymatic activity.

6zspAAA serine racemase bound to atp and malonate. (see paper)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:310/320 of 6zspAAA

query
sites
6zspAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S
|
S

T
x
S

S
x
I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S
x
K

T
|
T

G

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

S

-

Q

-

V

-

E

-

R

K

D

P

R

K

G

A

V

V

I

V

A

T

A

H

S
|
S

T
x
S

G

G

N
|
N

H
|
H

G

G

R
x
Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L
x
Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q
x
R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S

G

G

G

L

M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L

V

G

K

G
x
S

G

S

I

I

G

G

V

L

N

N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E
|
E

Q
x
R

E

M

R
x
K

E

L

I

L

V

I

E

E

G

P

A

T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G

G

Q

G

N
|
N

I

V

D

D

M

L

T

T

active site: K53 (= K51), S74 (≠ T76), E200 (≠ M209), A204 (≠ I213), D206 (≠ A215), G229 (≠ S230), L302 (= L303), S303 (= S304)
binding adenosine-5'-triphosphate: S28 (= S26), S29 (≠ T27), I30 (≠ S28), K48 (≠ S46), T49 (= T47), Q79 (≠ R81), Y111 (≠ L113), E266 (= E270), R267 (≠ Q271), K269 (≠ R273), N306 (= N307)
binding magnesium ion: E200 (≠ M209), A204 (≠ I213), D206 (≠ A215)
binding malonate ion: K53 (= K51), S73 (= S75), S74 (≠ T76), N76 (= N78), H77 (= H79), R125 (≠ Q128), G229 (≠ S230), S232 (≠ G233)

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/322 of 7nbgAAA

query
sites
7nbgAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G
|
G

R
x
Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I
|
I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K
|
K

V

K

A

L

E

A

I
|
I

R

Q

R

A

L
x
Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N

N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E

E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

M

L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (≠ S177), G183 (= G178), G184 (= G179), G185 (= G180), M186 (≠ L181), G236 (≠ S230), V237 (≠ L231), T282 (≠ A279), S310 (= S304), G311 (= G305)
binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ T76), G85 (= G80), Q86 (≠ R81), I101 (= I96), K111 (= K106), I115 (= I110), Y118 (≠ L113)

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/323 of 7nbfAAA

query
sites
7nbfAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L
x
H

R
x
L

T
|
T

P
|
P

L

V

T
x
L

I
x
T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R
x
F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G

G

R

Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L

Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N
|
N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E

E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

M

L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding magnesium ion: N244 (= N238)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (≠ S177), G183 (= G178), G184 (= G179), G185 (= G180), M186 (≠ L181), G236 (≠ S230), V237 (≠ L231), T282 (≠ A279), S310 (= S304), G311 (= G305)
binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: H21 (≠ L19), L22 (≠ R20), T23 (= T21), P24 (= P22), L26 (≠ T24), T27 (≠ I25), F46 (≠ R44)

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)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/323 of 7nbdAAA

query
sites
7nbdAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G

G

R

Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L

Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N
|
N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y
x
W

E

E

Q

R

E

M

R

K

E

L

I
x
L

V

I

E
|
E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I
x
V

D

D

M
x
L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (≠ Y269), L278 (≠ I275), V314 (≠ I308), L316 (≠ M310)
binding magnesium ion: N244 (= N238)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (≠ S177), G183 (= G178), G184 (= G179), G185 (= G180), M186 (≠ L181), G236 (≠ S230), V237 (≠ L231), E280 (= E277), T282 (≠ A279), S310 (= S304), G311 (= G305)

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)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/323 of 7nbcCCC

query
sites
7nbcCCC

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A
x
T

A
x
H

S

S

T
x
S

G

G

N
|
N

H
|
H

G

G

R

Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L

Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I
x
V

P
x
H

P
|
P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N

N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E

E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

M

L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding biphenyl-4-ylacetic acid: T78 (≠ A73), H79 (≠ A74), H84 (= H79), V148 (≠ I143), H149 (≠ P144), P150 (= P145)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (≠ S177), G183 (= G178), G184 (= G179), G185 (= G180), M186 (≠ L181), G236 (≠ S230), V237 (≠ L231), T282 (≠ A279), S310 (= S304), G311 (= G305)

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/323 of 7nbcAAA

query
sites
7nbcAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G

G

R

Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L

Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S
x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N
|
N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E

E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

M

L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding magnesium ion: N244 (= N238)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N83 (= N78), G182 (≠ S177), G183 (= G178), G184 (= G179), G185 (= G180), M186 (≠ L181), G236 (≠ S230), V237 (≠ L231), T282 (≠ A279), S310 (= S304), G311 (= G305)

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)
34% identity, 97% coverage: 2:311/321 of query aligns to 4:317/320 of 7nbhAAA

query
sites
7nbhAAA

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-

P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N

N

H

H

G
|
G

R
x
Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K
|
K

V

K

A

L

E

A

I
|
I

R

Q

R

A

L
x
Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

V

P

H

P

P

F

N

D

Q

H

E

P

P

H

A

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

V

P

P

E

L

V

V

A

D

T

A

V

L

L

V

V

V

P

P

L

V

S

G

G

G

L

M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D
|
D

S
x
G

L

V

G

K

G

S

I

I

G

G

V

L

N

N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E

E

G
x
P

A

T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G

G

Q

G

N
|
N

I
x
V

D
|
D

M

L

T

T

active site: K53 (= K51), S81 (≠ T76), E207 (≠ M209), A211 (≠ I213), D213 (≠ A215), G236 (≠ S230), L309 (= L303), S310 (= S304)
binding calcium ion: E207 (≠ M209), A211 (≠ I213), D213 (≠ A215)
binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ T76), G85 (= G80), Q86 (≠ R81), K111 (= K106), I115 (= I110), Y118 (≠ L113), D235 (= D229), P281 (≠ G278), N313 (= N307), V314 (≠ I308), D315 (= D309)

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)
34% identity, 97% coverage: 2:311/321 of query aligns to 7:320/340 of Q9GZT4

query
sites
Q9GZT4

I

I

S

S

H

F

D

A

L

D

I

V

K
x
E

Q

K

A

A

R

H

E

I

R

N

I

I

A

R

S

D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S
|
S

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x
S

S
x
I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S
x
K

T
|
T

G

G

S

S

F

F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

-

V

-
x
P

S

D

Q

A

V

L

E

E

R

R

D

K

-

P

R

K

G

A

V

V

I

V

A
x
T

A

H

S

S

T

S

G

G

N
|
N

H

H

G

G

R
x
Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I

I

C

V

M

V

S

P

R

Q

L

T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L
x
Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

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P

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P

P

F

N

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P

H

A

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V

I

I

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A

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G

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Q

G

G

T

T

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I

G

A

L

L

E

E

I

V

V

L

E

N

E

Q

M

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P

E

L

V

V

A
x
D

T

A

V

L

L

V

V

V

P

P

L

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x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

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V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

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T

L

I

A

A

D

D

S

G

L

V

G

K

G

S

I

I

G

G

V

L

N
|
N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R
x
K

E

L

I

L

V

I

E

E

G

P

A

T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L

L

S
|
S

G

G

Q

G

N
|
N

I

V

D

D

M

L

T

T

E13 (≠ K8) binding Mg(2+)
S31 (= S26) binding ATP
S32 (≠ T27) binding ATP
I33 (≠ S28) binding ATP
K51 (≠ S46) binding ATP
T52 (= T47) binding ATP
K56 (= K51) modified: N6-(pyridoxal phosphate)lysine
P69 (vs. gap) binding Ca(2+)
T81 (≠ A73) binding Ca(2+)
N86 (= N78) binding pyridoxal 5'-phosphate
Q89 (≠ R81) binding ATP
Y121 (≠ L113) binding ATP
D178 (≠ A170) binding Mg(2+)
G185 (≠ S177) binding pyridoxal 5'-phosphate
G186 (= G178) binding pyridoxal 5'-phosphate
G187 (= G179) binding pyridoxal 5'-phosphate
G188 (= G180) binding pyridoxal 5'-phosphate
M189 (≠ L181) binding pyridoxal 5'-phosphate
E210 (≠ M209) binding Ca(2+); binding Mg(2+); binding Mn(2+)
A214 (≠ I213) binding Ca(2+); binding Mg(2+); binding Mn(2+)
D216 (≠ A215) binding Ca(2+); binding Mg(2+); binding Mn(2+)
N247 (= N238) binding Ca(2+); binding Mg(2+)
K279 (≠ R273) binding ATP
S313 (= S304) binding pyridoxal 5'-phosphate
N316 (= N307) binding ATP

P04968 L-threonine dehydratase biosynthetic IlvA; Threonine deaminase; EC 4.3.1.19 from Escherichia coli (strain K12) (see paper)
37% identity, 90% coverage: 21:310/321 of query aligns to 32:321/514 of P04968

query
sites
P04968

T

T

P

P

L

L

T

Q

I

K

S

M

T

E

S

K

L

L

S

S

E

S

R

R

T

L

G

D

A

N

Q

V

V

I

S

L

L

V

K

K

L

R

E

E

H

D

R

R

Q

Q

S

P

T

V

G

H

S

S

F

F

K
|
K

L

L

R

R

G

G

A

A

T

Y

N

A

A

M

V

M

L

A

Q

G

L

L

S

T

Q

E

V

E

E

Q

R

K

D

A

R

H

G

G

V

V

I

I

A

T

A

A

S

S

T

A

G

G

N
|
N

H

H

G

A

R

Q

A

G

L

V

S

A

Y

F

A

S

R

A

A

R

V

L

G

G

S

V

C

K

A

A

T

L

I

I

C

V

M

M

S

P

R

T

L

A

V

T

P

A

E

D

N

I

K

K

V

V

A

D

E

A

I

V

R

R

R

G

L

F

G

G

A

G

T

E

V

V

R

L

I

L

V

H

G

G

S

A

S

N

Q

F

D

D

D

E

A

A

Q

K

A

A

E

K

V

A

E

I

R

E

Q

L

V

S

A

Q

E

Q

G

G

L

F

S

T

M

W

I

V

P

P

F

F

D

D

H

H

P

P

H

M

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

L

G

A

L

L

E

E

I

L

V

L

E

Q

M

D

P

A

E

H

V

L

A

D

T

R

V

V

L

F

V

V

P

P

L

V

S
x
G

G
|
G

L
|
L

A

A

G

G

V

V

A

A

A

V

A

L

V

I

K

K

T

Q

I

L

R

M

P

P

Q

Q

A

I

K

K

V

V

I

I

G

A

V

V

T

E

M

A

D

E

R

D

G

S

A

A

A

C

M

L

K

K

A

A

S

A

I

L

D

D

A

A

G

G

H

H

P

P

V

V

Q

D

V

L

K

P

E

R

Y

V

R

G

S

L

L

F

A

A

D

E

S

-

L

-

G

-

G

G

I

V

G

A

V

V

N

K

N

R

-

I

-

G

T

D

W

E

T

T

F

F

P

R

M

L

C

C

K

Q

T

E

L

Y

L

L

D

D

I

I

V

I

L

T

V

V

N

D

E

S

G

D

E

A

I

I

A

C

A

A

G

A

V

M

R

K

H

D

A

L

Y

F

E

E

Q

D

E

V

R

R

E

A

I

V

V

A

E

E

G

P

A

S

G

G

A

A

V

L

G

A

I

L

A

A

A

G

L

M

L

K

S

K

G

Y

-

I

K

A

L

L

A

H

H

N

L

I

K

R

G

G

P

E

-

R

A

L

A

A

V

H

I

I

L

L

S
|
S

G

G

Q

A

N

N

I

V

D

N

M

F

K62 (= K51) modified: N6-(pyridoxal phosphate)lysine
N89 (= N78) binding pyridoxal 5'-phosphate
GGGGL 188:192 (≠ SGGGL 177:181) binding pyridoxal 5'-phosphate
S315 (= S304) binding pyridoxal 5'-phosphate

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
34% identity, 96% coverage: 2:309/321 of query aligns to 4:310/310 of 7nbgDDD

query
sites
7nbgDDD

I

I

S

S

H

F

D

A

L

D

I

V

K

E

Q

K

A

A

R

H

E

I

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N

I

I

A

R

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D

H

S

V

I

L

H

R

L

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

I

L

L

S

N

E

Q

R

L

T

T

G

G

A

R

Q

N

V

L

S

F

L

F

K

K

L

C

E

E

H

L

R

F

Q

Q

S

K

T

T

G

G

S

S

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

L

N

N

A

A

V

V

L

R

Q

S

L

L

S

-

Q

-

V

V

E

R

R

K

D

P

R

K

G

A

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G

G

R
x
Q

A

A

L

L

S

T

Y

Y

A

A

R

K

A

L

V

E

G

G

S

I

C

P

A

A

T

Y

I
|
I

C

V

M

V

S

P

R

Q

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T

V

A

P

P

E

D

N

C

K

K

V

K

A

L

E

A

I

I

R

Q

R

A

L
x
Y

G

G

A

A

T

S

V

I

R

-

I

V

V

Y

G

C

S

E

S

P

Q

S

D

D

D

E

A

S

Q

R

A

E

E

N

V

V

E

A

R

K

Q

R

V

V

A

T

E

E

-

E

-

T

E

E

G

G

L

I

S

-

M

M

I

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P

H

P

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N

D

Q

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E

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P

H

A

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V

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I

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A

G

G

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Q

G

G

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G

A

L

L

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E

I

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V

L

E

N

E

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M

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P

E

L

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V

A

D

T

A

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L

L

V

V

V

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P

L

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x
G

G
|
G

L
x
M

A

L

A

A

G

G

V

I

A

A

A

I

A

T

V

V

K

K

T

A

I

L

R

K

P

P

Q

S

A

V

K

K

V

V

I

Y

G

-

V

-

T

-

M

-

D

-

R

-

G

-

A

A

M
x
E

K

P

A

S

S

N

I
x
A

D

D

A
x
D

G

C

H

Y

P

Q

V

S

Q

K

V

L

K

K

-

G

-

K

-

L

-

M

-

P

-

N

-

L

-

Y

E

P

Y

P

R

E

S

T

L

I

A

A

D

D

S
x
G

L
x
V

G

K

G

S

I

I

G

G

V

L

N
|
N

N

-

T

-

W

-

T

T

F

W

P

P

M

I

C

I

K

R

T

D

L

L

L

V

D

D

I

I

V

F

L

T

V

V

N

T

E

E

G

D

E

E

I

I

A

K

A

C

G

A

V

T

R

Q

H

L

A

V

Y

W

E

E

Q

R

E

M

R

K

E

L

I

L

V

I

E
|
E

G

P

A
x
T

G

A

A

G

V

V

G

G

I

V

A

A

L

V

L

L

S

S

G

Q

K

H

L

F

A

Q

H

T

L

V

K

S

G

P

P

E

A

V

-

K

-

N

-

I

A

C

V

I

I

V

L
|
L

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

active site: K53 (= K51), S76 (≠ T76), E202 (≠ M209), A206 (≠ I213), D208 (≠ A215), G231 (≠ S230), L304 (= L303), S305 (= S304)
binding calcium ion: E202 (≠ M209), A206 (≠ I213), D208 (≠ A215)
binding magnesium ion: N239 (= N238)
binding ortho-xylene: S76 (≠ T76), Q81 (≠ R81), I96 (= I96), Y113 (≠ L113)
binding pyridoxal-5'-phosphate: F52 (= F50), K53 (= K51), N78 (= N78), G177 (≠ S177), G178 (= G178), G179 (= G179), G180 (= G180), M181 (≠ L181), G231 (≠ S230), V232 (≠ L231), E275 (= E277), T277 (≠ A279), S305 (= S304), G306 (= G305)

Sites not aligning to the query:

binding magnesium ion: 3

1tdjA Threonine deaminase (biosynthetic) from e. Coli (see paper)
37% identity, 90% coverage: 21:310/321 of query aligns to 28:317/494 of 1tdjA

query
sites
1tdjA

T

T

P

P

L

L

T

Q

I

K

S

M

T

E

S

K

L

L

S

S

E

S

R

R

T

L

G

D

A

N

Q

V

V

I

S

L

L

V

K

K

L

R

E

E

H

D

R

R

Q

Q

S

P

T

V

G

H

S

S

F
|
F

K
|
K

L

L

R

R

G

G

A

A

T

Y

N

A

A

M

V

M

L

A

Q

G

L

L

S

T

Q

E

V

E

E

Q

R

K

D

A

R

H

G

G

V

V

I

I

A

T

A

A

S

S

T
x
A

G

G

N
|
N

H

H

G

A

R

Q

A

G

L

V

S

A

Y

F

A

S

R

A

A

R

V

L

G

G

S

V

C

K

A

A

T

L

I

I

C

V

M

M

S

P

R

T

L

A

V

T

P

A

E

D

N

I

K

K

V

V

A

D

E

A

I

V

R

R

R

G

L

F

G

G

A

G

T

E

V

V

R

L

I

L

V

H

G

G

S

A

S

N

Q

F

D

D

D

E

A

A

Q

K

A

A

E

K

V

A

E

I

R

E

Q

L

V

S

A

Q

E

Q

G

G

L

F

S

T

M

W

I

V

P

P

F

F

D

D

H

H

P

P

H

M

V

V

I

I

T

A

G

G

Q

Q

G

G

T

T

V

L

G

A

L

L

E

E

I

L

V

L

E

Q

M

D

P

A

E

H

V

L

A

D

T

R

V

V

L

F

V

V

P

P

L

V

S
x
G

G
|
G

L

L

A

A

G

G

V

V

A

A

A

V

A

L

V

I

K

K

T

Q

I

L

R

M

P

P

Q

Q

A

I

K

K

V

V

I

I

G

A

V

V

T
x
E

M

A

D

E

R

D

G
x
S

A

A

A
x
C

M

L

K

K

A

A

S

A

I

L

D

D

A

A

G

G

H

H

P

P

V

V

Q

D

V

L

K

P

E

R

Y

V

R

G

S

L

L

F

A

A

D

E

S

-

L

-

G

-

G
|
G

I

V

G

A

V

V

N

K

N

R

-

I

-

G

T

D

W

E

T

T

F

F

P

R

M

L

C

C

K

Q

T

E

L

Y

L

L

D

D

I

I

V

I

L

T

V

V

N

D

E

S

G

D

E

A

I

I

A

C

A

A

G

A

V

M

R

K

H

D

A

L

Y

F

E

E

Q

D

E

V

R

R

E

A

I

V

V

A

E
|
E

G

P

A

S

G

G

A

A

V

L

G

A

I

L

A

A

A

G

L

M

L

K

S

K

G

Y

-

I

K

A

L

L

A

H

H

N

L

I

K

R

G

G

P

E

-

R

A

L

A

A

V

H

I

I

L
|
L

S
|
S

G
|
G

Q

A

N

N

I

V

D

N

M

F

active site: K58 (= K51), A83 (≠ T76), E209 (≠ T202), S213 (≠ G206), C215 (≠ A208), G237 (= G234), L310 (= L303), S311 (= S304)
binding pyridoxal-5'-phosphate: F57 (= F50), K58 (= K51), N85 (= N78), G184 (≠ S177), G185 (= G178), G186 (= G179), G187 (= G180), G237 (= G234), E282 (= E277), S311 (= S304), G312 (= G305)

O59791 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
33% identity, 96% coverage: 3:310/321 of query aligns to 9:314/323 of O59791

query
sites
O59791

S

T

H

Y

D

D

L

D

I

V

K

A

Q

S

A

A

R

S

E

E

R

R

I

I

A

K

S

K

H

F

V

A

L

N

R

K

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

T

L

V

S

N

E

K

R

E

T

F

G

V

A

A

Q

E

V

V

S

F

L

F

K

K

L

C

E

E

H

N

R

F

Q

Q

S

K

T

M

G

G

S

A

F

F

K
|
K

L

F

R

R

G

G

A

A

T

L

N

N

A

A

V

L

L

S

Q

Q

L

L

S

N

Q

E

V

A

E

Q

R

R

D

K

R

A

G

G

V

V

I

L

A

T

A

F

S

S

T
x
S

G

G

N
|
N

H

H

G

A

R

Q

A

A

L

I

S

A

Y

L

A

S

A

A

R

K

A

I

V

L

G

G

S

I

C

P

A

A

T

K

I

I

C

I

M

M

S

P

R

L

L

D

V

A

P

P

E

E

N

A

K

K

V

V

A

A

E

A

I

T

R

K

R

G

L

Y

G

G

A

G

T

Q

V

V

R

I

I

M

V

Y

G

D

S

R

S

Y

Q

K

D

D

A

R

Q

E

A

K

E

M

V

A

E

K

R

E

Q

I

V

S

A

E

E

R

E

E

G

G

L

L

S

T

M

I

I

I

P

P

F

Y

D

D

H

H

P

P

H

H

V

V

I

L

T

A

G

G

Q

Q

G

G

T

T

V

A

G

A

L

K

E

E

I

L

V

F

E

E

M

V

P

G

E

P

V

L

A

D

T

A

V

L

L

F

V

V

P

C

L

L

S
x
G

G
|
G

L
|
L

A

L

A

S

G

G

V

S

A

A

A

L

A

A

V

A

K

R

T

H

I

F

R

A

P

P

Q

N

A

C

K

E

V

V

I

Y

G

G

V

V

T
x
E

M

P

D

E

R

A

G
|
G

A

N

A
x
D

M

G

K

Q

A

Q

S

S

I

F

D

R

A

K

G

G

H

S

P

I

V

V

Q

H

V

I

K

D

E

T

Y

P

R

K

S

T

L

I

A

A

D

D

S

-

L

-

G

G

G

A

G

Q

I

T

G

Q

V

H

N

L

N

G

T

N

W

Y

T

T

F

F

P

S

M

I

C

I

K

K

T

E

L

K

L

V

D

D

I

I

V

L

L

T

V

V

N

S

E

D

G

E

E

E

I

L

A

I

A

D

G

C

V

L

R

K

H

F

A

Y

Y

A

E

A

Q

R

E

M

R

K

E

I

I

V

V

V

E

E

G

P

A

T

G

G

A

C

V

L

G

S

I

F

A

A

L

A

L

R

S

A

G

M

K

K

L

E

A

K

H

L

L

K

K

N

G

K

P

R

A

I

A

G

V

I

I

I

L

I

S
|
S

G

G

Q

G

N

N

I

V

D

D

M

I

K57 (= K51) active site, Proton acceptor; modified: Lysino-D-alanine (Lys); alternate; modified: N6-(pyridoxal phosphate)lysine; alternate
S82 (≠ T76) 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 (= N78) binding pyridoxal 5'-phosphate
G183 (≠ S177) binding pyridoxal 5'-phosphate
G184 (= G178) binding pyridoxal 5'-phosphate
G185 (= G179) binding pyridoxal 5'-phosphate
G186 (= G180) binding pyridoxal 5'-phosphate
L187 (= L181) binding pyridoxal 5'-phosphate
E208 (≠ T202) binding Mg(2+)
G212 (= G206) binding Mg(2+)
D214 (≠ A208) binding Mg(2+)
S308 (= S304) binding pyridoxal 5'-phosphate

5cvcA Structure of maize serine racemase (see paper)
35% identity, 95% coverage: 5:310/321 of query aligns to 6:313/329 of 5cvcA

query
sites
5cvcA

D

D

L

S

I

I

K

R

Q

E

A

A

R

Q

E

A

R

R

I

I

A

A

S

P

H

Y

V

V

L

H

R

R

T

T

P

P

L

V

T

M

I

S

S

S

T

T

S

S

L

I

S

D

E

A

R

M

T

V

G

G

A

K

Q

K

V

L

S

F

L

F

K

K

L

C

E

E

H

C

R

F

Q

Q

S

K

T

A

G

G

S

A

F
|
F

K
|
K

L

I

R

R

G

G

A

A

T

S

N

N

A

S

V

I

L

F

Q

A

L

L

S

D

Q

D

V

E

E

Q

R

V

D

S

R

K

G

G

V

V

I

V

A

T

A

H

S

S

T
x
S

G

G

N
|
N

H

H

G

A

R

A

A

A

L

V

S

A

Y

L

A

A

R

K

A

L

V

R

G

G

S

I

C

P

A

A

T

H

I

I

C

V

M

I

S

P

R

R

L

N

V

A

P

P

E

A

N

S

K

K

V

V

A

E

E

N

I

V

R

K

R

C

L

Y

G

G

A

G

T

H

V

I

R

-

I

I

V

W

G

S

S

D

S

A

Q

S

D

I

D

E

A

S

Q

R

A

E

E

Y

V

V

E

S

R

K

Q

R

V

V

A

Q

E

E

-

T

G

G

L

A

S

V

M

L

I

I

P

H

P

P

F

I

D

N

H

S

P

K

H

Y

V

T

I

I

T

S

G

G

Q

Q

G

G

T

T

V

V

G

S

L

L

E

E

I

L

V

L

E

E

E

Q

M

V

P

P

E

E

V

I

A

D

T

T

V

I

L

I

V

V

P

P

L

I

S
|
S

G
|
G

L

L

A

I

A

S

G

G

V

V

A

A

A

L

A

A

V

A

K

K

T

A

I

I

R

N

P

P

Q

S

A

I

K

R

V

I

I

L

G

A

V

A

T
x
E

-

P

-

K

-

G

M
x
A

D

D

R
x
D

G

S

A

A

A

Q

M

S

K

K

A

A

S

-

I

-

D

-

A

A

G

G

H

K

P

I

V

I

Q

T

V

L

K

P

E

S

Y

T

R

N

S

T

L

I

A

A

D

D

S
x
G

L
|
L

G

R

G

A

G

F

I

L

G

G

V

-

N

D

N

L

T

T

W

W

T

-

F

-

P

P

M

V

C

V

K

R

T

D

L

L

L

V

D

D

I

V

V

I

L

V

V

V

N

D

E

D

G

T

E

A

I

I

A

V

A

D

G

A

V

M

R

K

H

M

A

C

Y

Y

E

E

Q

I

E

L

R

K

E

V

I

A

V

V

E
|
E

G

P

A

S

G

G

A

A

V

I

G

G

I

L

A

A

L

A

L

L

S

S

G

D

K

E

L

F

A

K

-

Q

-

S

-

A

-

W

H

H

L

E

K

S

G

S

P

K

A

I

A

G

V

I

I

I

L
x
V

S
|
S

G
|
G

Q

G

N

N

I

V

D

D

M

L

active site: K52 (= K51), S77 (≠ T76), E203 (≠ T202), A207 (≠ M203), D209 (≠ R205), G231 (≠ S230), V306 (≠ L303), S307 (= S304)
binding magnesium ion: E203 (≠ T202), A207 (≠ M203), D209 (≠ R205)
binding pyridoxal-5'-phosphate: F51 (= F50), K52 (= K51), N79 (= N78), S178 (= S177), G179 (= G178), G180 (= G179), G181 (= G180), L232 (= L231), E275 (= E277), S307 (= S304), G308 (= G305)

2zr8A Crystal structure of modified serine racemase complexed with serine (see paper)
33% identity, 96% coverage: 3:310/321 of query aligns to 5:310/319 of 2zr8A

query
sites
2zr8A

S

T

H

Y

D

D

L

D

I

V

K

A

Q

S

A

A

R

S

E

E

R

R

I

I

A

K

S

K

H

F

V

A

L

N

R

K

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

T

L

V

S

N

E

K

R

E

T

F

G

V

A

A

Q

E

V

V

S

F

L

F

K

K

L

C

E

E

H

N

R

F

Q

Q

S

K

T

M

G

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

T

L

N

N

A

A

V

L

L

S

Q

Q

L

L

S

N

Q

E

V

A

E

Q

R

R

D

K

R

A

G

G

V

V

I

L

A

T

A

F

S
|
S

T
x
S

G

G

N
|
N

H
|
H

G

A

R

Q

A

A

L

I

S

A

Y

L

A

S

A

A

R

K

A

I

V

L

G

G

S

I

C

P

A

A

T

K

I

I

C

I

M

M

S

P

R

L

L

D

V

A

P

P

E

E

N

A

K

K

V

V

A

A

E

A

I

T

R

K

R

G

L

Y

G

G

A

G

T

Q

V

V

R

I

I

M

V

Y

G

D

S

R

S

Y

Q

K

D

D

A
x
R

Q

E

A

K

E

M

V

A

E

K

R

E

Q

I

V

S

A

E

E

R

E

E

G

G

L

L

S

T

M

I

I

I

P

P

P
|
P

F

Y

D

D

H

H

P

P

H

H

V

V

I

L

T

A

G

G

Q

Q

G

G

T

T

V

A

G

A

L

K

E

E

I

L

V

F

E

E

M

V

P

G

E

P

V

L

A

D

T

A

V

L

L

F

V

V

P

C

L

L

S
x
G

G
|
G

L

L

A

L

A

S

G

G

V

S

A

A

A

L

A

A

V

A

K

R

T

H

I

F

R

A

P

P

Q

N

A

C

K

E

V

V

I

Y

G

G

V

V

T
x
E

M

P

D

E

R

A

G
|
G

A

N

A
x
D

M

G

K

Q

A

Q

S

S

I

F

D

R

A

K

G

G

H

S

P

I

V

V

Q

H

V

I

K

D

E

T

Y

P

R

K

S

T

L

I

A

A

D
|
D

S

-

L

-

G
|
G

G
x
A

G
x
Q

I
x
T

G

Q

V

H

N

L

N

G

T

N

W

Y

T

T

F

F

P

S

M

I

C

I

K

K

T

E

L

K

L

V

D

D

I

I

V

L

L

T

V

V

N

S

E

D

G

E

E

E

I

L

A

I

A

D

G

C

V

L

R

K

H

F

A

Y

Y

A

E

A

Q

R

E

M

R

K

E

I

I

V

V

V

E
|
E

G

P

A
x
T

G

G

A

C

V

L

G

S

I

F

A

A

L

A

L

R

S

A

G

M

K

K

L

E

A

K

H

L

L

K

K

N

G

K

P

R

A

I

A

G

V

I

I

I

L
x
I

S
|
S

G

G

Q

G

N

N

I

V

D

D

M

I

active site: K53 (= K51), S78 (≠ T76), E204 (≠ T202), G208 (= G206), D210 (≠ A208), G232 (= G232), I303 (≠ L303), S304 (= S304)
binding magnesium ion: E204 (≠ T202), G208 (= G206), D210 (≠ A208)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F50), K53 (= K51), S77 (= S75), S78 (≠ T76), N80 (= N78), H81 (= H79), P147 (= P145), G179 (≠ S177), G180 (= G178), G181 (= G179), G182 (= G180), G232 (= G232), E277 (= E277), T279 (≠ A279), S304 (= S304)
binding serine: S78 (≠ T76), R129 (≠ A127), D231 (= D229), G232 (= G232), A233 (≠ G233), Q234 (≠ G234), T235 (≠ I235)

2zpuA Crystal structure of modified serine racemase from s.Pombe. (see paper)
33% identity, 96% coverage: 3:310/321 of query aligns to 5:310/319 of 2zpuA

query
sites
2zpuA

S

T

H

Y

D

D

L

D

I

V

K

A

Q

S

A

A

R

S

E

E

R

R

I

I

A

K

S

K

H

F

V

A

L

N

R

K

T

T

P

P

L

V

T

L

I

T

S

S

T

S

S

T

L

V

S

N

E

K

R

E

T

F

G

V

A

A

Q

E

V

V

S

F

L

F

K

K

L

C

E

E

H

N

R

F

Q

Q

S

K

T

M

G

G

S

A

F
|
F

K
|
K

L

F

R

R

G

G

A

A

T

L

N

N

A

A

V

L

L

S

Q

Q

L

L

S

N

Q

E

V

A

E

Q

R

R

D

K

R

A

G

G

V

V

I

L

A

T

A

F

S
|
S

T
x
S

G

G

N
|
N

H
|
H

G

A

R

Q

A

A

L

I

S

A

Y

L

A

S

A

A

R

K

A

I

V

L

G

G

S

I

C

P

A

A

T

K

I

I

C

I

M

M

S

P

R

L

L

D

V

A

P

P

E

E

N

A

K

K

V

V

A

A

E

A

I

T

R

K

R

G

L

Y

G

G

A

G

T

Q

V

V

R

I

I

M

V

Y

G

D

S

R

S

Y

Q

K

D

D

A

R

Q

E

A

K

E

M

V

A

E

K

R

E

Q

I

V

S

A

E

E

R

E

E

G

G

L

L

S

T

M

I

I

I

P

P

P
|
P

F

Y

D

D

H

H

P

P

H

H

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V

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L

T

A

G

G

Q

Q

G

G

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G

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D

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G

G
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G

L

L

A

L

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G

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S

A

A

A

L

A

A

V

A

K

R

T

H

I

F

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A

P

P

Q

N

A

C

K

E

V

V

I

Y

G

G

V

V

T
x
E

M

P

D

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A

G
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G

A

N

A
x
D

M

G

K

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A

Q

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S

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D

R

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K

G

G

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V

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V

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K

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Y

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A

A

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D

S

-

L

-

G
|
G

G

A

G

Q

I

T

G

Q

V

H

N

L

N

G

T

N

W

Y

T

T

F

F

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M

I

C

I

K

K

T

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L

K

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D

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E

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T

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L

A

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K

K

L

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A

K

H

L

L

K

K

N

G

K

P

R

A

I

A

G

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I

I

I

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x
I

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S

G

G

Q

G

N

N

I

V

D

D

M

I

active site: K53 (= K51), S78 (≠ T76), E204 (≠ T202), G208 (= G206), D210 (≠ A208), G232 (= G232), I303 (≠ L303), S304 (= S304)
binding magnesium ion: E204 (≠ T202), G208 (= G206), D210 (≠ A208)
binding n-(5'-phosphopyridoxyl)-d-alanine: F52 (= F50), K53 (= K51), S77 (= S75), S78 (≠ T76), N80 (= N78), H81 (= H79), P147 (= P145), G179 (≠ S177), G180 (= G178), G181 (= G179), G182 (= G180), G232 (= G232), E277 (= E277), T279 (≠ A279), S304 (= S304)

Query Sequence

>WP_015886807.1 NCBI__GCF_000018545.1:WP_015886807.1
MISHDLIKQARERIASHVLRTPLTISTSLSERTGAQVSLKLEHRQSTGSFKLRGATNAVL
QLSQVERDRGVIAASTGNHGRALSYAARAVGSCATICMSRLVPENKVAEIRRLGATVRIV
GSSQDDAQAEVERQVAEEGLSMIPPFDHPHVITGQGTVGLEIVEEMPEVATVLVPLSGGG
LAAGVAAAVKTIRPQAKVIGVTMDRGAAMKASIDAGHPVQVKEYRSLADSLGGGIGVNNT
WTFPMCKTLLDDIVLVNEGEIAAGVRHAYEQEREIVEGAGAVGIAALLSGKLAHLKGPAA
VILSGQNIDMTLHRKIVNGRI

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