SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_013835261.1 NCBI__GCF_000214825.1:WP_013835261.1 to proteins with known functional sites using BLASTp with E ≤ 0.001.

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

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

3undB Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from burkholderia pseudomallei (see paper)
51% identity, 95% coverage: 5:269/279 of query aligns to 11:277/284 of 3undB

query
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3undB

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binding arabinose-5-phosphate: N27 (≠ C21), K61 (= K55), N63 (= N57), R64 (= R58), S65 (= S59), H203 (= H195), Q206 (= Q198), R208 (≠ P200), A214 (≠ T206), S215 (= S207), C250 (≠ S242), D251 (= D243)
binding 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid: K56 (= K50), K61 (= K55), N63 (= N57), R64 (= R58), S65 (= S59), K139 (= K133), H203 (= H195), R208 (≠ P200), A214 (≠ T206), S215 (= S207), D251 (= D243)
binding phosphoenolpyruvate: K56 (= K50), Q114 (= Q108), P116 (= P110), A117 (= A111), K139 (= K133), R169 (= R163), H203 (= H195)

1g7vA Crystal structures of kdo8p synthase in its binary complexes with the mechanism-based inhibitor (see paper)
48% identity, 96% coverage: 7:274/279 of query aligns to 12:279/284 of 1g7vA

query
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1g7vA

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active site: N26 (≠ C21), K60 (= K55), D250 (= D243)
binding {[(2,2-dihydroxy-ethyl)-(2,3,4,5-tetrahydroxy-6-phosphonooxy-hexyl)-amino]-methyl}-phosphonic acid: N62 (= N57), R63 (= R58), F117 (= F112), R168 (= R163), H202 (= H195), Q205 (= Q198), A247 (= A240), G251 (= G244), P252 (= P245)

1g7uA Crystal structures of kdo8p synthase in its binary complex with substrate phosphoenol pyruvate (see paper)
47% identity, 96% coverage: 7:274/279 of query aligns to 12:279/284 of 1g7uA

query
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1g7uA

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binding phosphoenolpyruvate: F117 (= F112), R168 (= R163), H202 (= H195)

3e0iA Cu2+ substituted aquifex aeolicus kdo8ps in complex with pep (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 3e0iA

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3e0iA

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binding copper (ii) ion: C10 (= C21), H184 (= H195), E221 (= E232)
binding phosphoenolpyruvate: K40 (= K50), K45 (= K55), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)
binding phosphate ion: R48 (= R58), S49 (= S59), K195 (≠ T206), S196 (= S207)

2a21A Aquifex aeolicus kdo8ps in complex with pep, po4, and zn2+ (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 2a21A

query
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2a21A

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G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T

K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E
|
E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding phosphoenolpyruvate: K40 (= K50), K45 (= K55), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)
binding phosphate ion: R48 (= R58), S49 (= S59), S196 (= S207)
binding zinc ion: C10 (= C21), H184 (= H195), E221 (= E232), D232 (= D243)

1jcyA Aquifex aeolicus kdo8p synthase in complex with r5p, pep and cadmium (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 1jcyA

query
sites
1jcyA

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q
|
Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T

K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D

D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding phosphoenolpyruvate: K40 (= K50), K45 (= K55), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)
binding ribose-5-phosphate: N47 (= N57), R48 (= R58), S49 (= S59), H184 (= H195), Q187 (= Q198), S196 (= S207)

1fwwA Aquifex aeolicus kdo8p synthase in complex with pep, a5p and cadmium (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 1fwwA

query
sites
1fwwA

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T

K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding arabinose-5-phosphate: N47 (= N57), R48 (= R58), S49 (= S59), H184 (= H195), S196 (= S207), D232 (= D243)
binding phosphoenolpyruvate: K40 (= K50), K45 (= K55), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)

1fwtA Aquifex aeolicus kdo8p synthase in complex with pep, e4p and cadmium (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 1fwtA

query
sites
1fwtA

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T

K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D

D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding erythose-4-phosphate: N47 (= N57), R48 (= R58), S49 (= S59), S196 (= S207)
binding phosphoenolpyruvate: K40 (= K50), K45 (= K55), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)

2nx3D Structural and mechanistic changes along an engineered path from metallo to non-metallo kdo8p synthase (see paper)
48% identity, 92% coverage: 14:270/279 of query aligns to 2:258/262 of 2nx3D

query
sites
2nx3D

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C
x
N

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K

K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T
x
K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

P

N

T

M

A

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding (2r,4r,5r,6r,7r)-2,4,5,6,7-pentahydroxy-2,8-bis(phosphonooxy)octanoic acid: N9 (≠ C21), K44 (= K55), N46 (= N57), R47 (= R58), S48 (= S59), Q97 (= Q108), P99 (= P110), A100 (= A111), K122 (= K133), R152 (= R163), H183 (= H195), K194 (≠ T206), S195 (= S207), D231 (= D243)

2nx1A Structural and mechanistic changes along an engineered path from metallo to non-metallo kdo8p synthase (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:259/263 of 2nx1A

query
sites
2nx1A

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

N

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

L

G

G

S

D

T

K

S
|
S

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding phosphoenolpyruvate: K40 (= K50), Q98 (= Q108), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195)
binding 5-O-phosphono-beta-D-ribofuranose: K45 (= K55), N47 (= N57), R48 (= R58), S49 (= S59), S196 (= S207), D232 (= D243)

1x6uA Kdo8p synthase in it's binary complex with the product kdo8p (see paper)
46% identity, 96% coverage: 7:274/279 of query aligns to 12:267/272 of 1x6uA

query
sites
1x6uA

H

N

V

V

G

A

I

N

D

D

Q

L

P

P

F

F

F

V

L

L

I

F

A

G

G

G

P

M

C
x
N

V

V

I

L

E

E

S

S

E

R

Q

D

L

L

A

A

I

M

D

R

T

I

A

C

G

E

Q

H

L

Y

K

V

E

T

L

V

T

T

T

Q

R

K

L

L

G

G

I

I

P

P

F

Y

I

V

F

F

K
|
K

S

A

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R

R

S

S

T

I

A

H

S

S

F

Y

R

R

G

G

L

P

G

G

I

L

D

E

E

E

G

G

L

M

R

K

I

I

L

F

Q

Q

K

E

V

L

K

K

D

Q

E

T

I

F

G

G

V

V

P

K

V

I

L

I

T

T

D

D

V

V

H

H

E

E

D

P

T

S

P

Q

L

A

A

Q

E

P

V

V

A

A

S

D

V

V

D

D

V

V

M

I

Q
|
Q

T

L

P

P

A

A

F
|
F

L

L

V

A

R

R

Q

Q

T

T

N

D

F

L

I

V

Q

E

N

A

V

M

C

A

R

K

Q

T

G

G

L

A

P

V

V

I

N

N

I

V

K
|
K

K

K

G

P

Q

Q

F

F

Q

V

A

S

P

P

W

G

D

Q

M

M

D

G

Q

N

V

I

V

V

A

D

K

K

A

F

R

K

E

E

V

G

G

G

N

N

E

E

Q

K

I

V

M

I

I

L

C

C

D

D

R

R

G

G

T

A

S

N

F

F

G

G

Y

Y

N

D

T

N

L

L

I

V

S

V

D

D

M

M

R

L

G

G

L

F

A

S

S

I

M

M

R

K

T

V

-

S

-

G

G

N

C

S

P

P

V

V

V

I

F

F

D
|
D

A

V

T

T

H
|
H

S

A

V

L

Q

-

P

-

G

-

Q

-

G

-

S

-

T

-

S

-

G

-

Q

Q

R

R

E

A

F

Q

V

V

P

A

V

E

L

L

A

A

R

R

A

A

A

G

I

M

A

A

A

V

G

G

V

L

A

A

G

G

I

L

F
|
F

M

I

E
|
E

T

A

H

H

P

P

D

D

P

P

A

E

N

H

A

A

K

K

S

C

D
|
D

G

G

P
|
P

N

S

M

A

W

L

P

P

L

L

D

A

Q

K

L

L

E

E

P

P

V

F

L

L

A

K

V

Q

L

M

K

K

A

A

L

I

D

D

V

L

V

V

K

K

Q

-

H

-

G

G

F

F

V

E

E

E

active site: N26 (≠ C21), K60 (= K55), D238 (= D243)
binding 3-deoxy-8-O-phosphono-alpha-D-manno-oct-2-ulopyranosonic acid: N26 (≠ C21), K55 (= K50), N62 (= N57), Q113 (= Q108), F117 (= F112), K138 (= K133), D199 (= D192), H202 (= H195), F225 (= F230), E227 (= E232), P240 (= P245)

1phwA Crystal structure of kdo8p synthase in its binary complex with substrate analog 1-deoxy-a5p (see paper)
46% identity, 96% coverage: 7:274/279 of query aligns to 12:267/272 of 1phwA

query
sites
1phwA

H

N

V

V

G

A

I

N

D

D

Q

L

P

P

F

F

F

V

L

L

I

F

A

G

G

G

P

M

C
x
N

V

V

I

L

E

E

S

S

E

R

Q

D

L

L

A

A

I

M

D

R

T

I

A

C

G

E

Q

H

L

Y

K

V

E

T

L

V

T

T

T

Q

R

K

L

L

G

G

I

I

P

P

F

Y

I

V

F

F

K

K

S

A

S

S

Y

F

D

D

K
|
K

A

A

N

N

R

R

S

S

T

I

A

H

S

S

F

Y

R

R

G

G

L

P

G

G

I

L

D

E

E

E

G

G

L

M

R

K

I

I

L

F

Q

Q

K

E

V

L

K

K

D

Q

E

T

I

F

G

G

V

V

P

K

V

I

L

I

T

T

D

D

V

V

H

H

E

E

D

P

T

S

P

Q

L

A

A

Q

E

P

V

V

A

A

S

D

V

V

D

D

V

V

M

I

Q

Q

T

L

P
|
P

A
|
A

F
|
F

L

L

V

A

R

R

Q

Q

T

T

N

D

F

L

I

V

Q

E

N

A

V

M

C

A

R

K

Q

T

G

G

L

A

P

V

V

I

N

N

I

V

K
|
K

K

K

G

P

Q

Q

F

F

Q

V

A

S

P

P

W

G

D

Q

M

M

D

G

Q

N

V

I

V

V

A

D

K

K

A

F

R

K

E

E

V

G

G

G

N

N

E

E

Q

K

I

V

M

I

I

L

C

C

D

D

R
|
R

G

G

T

A

S

N

F

F

G

G

Y

Y

N

D

T

N

L

L

I

V

S

V

D

D

M

M

R

L

G

G

L

F

A

S

S

I

M

M

R

K

T

V

-

S

-

G

G

N

C

S

P

P

V

V

V

I

F

F

D

D

A

V

T

T

H
|
H

S

A

V

L

Q

-

P

-

G

-

Q

-

G

-

S

-

T

-

S

-

G

-

Q

Q

R

R

E

A

F

Q

V

V

P

A

V

E

L

L

A

A

R

R

A

A

A

G

I

M

A

A

A

V

G

G

V

L

A

A

G

G

I

L

F

F

M

I

E

E

T

A

H

H

P

P

D

D

P

P

A

E

N

H

A

A

K

K

S

C

D
|
D

G

G

P

P

N

S

M

A

W

L

P

P

L

L

D

A

Q

K

L

L

E

E

P

P

V

F

L

L

A

K

V

Q

L

M

K

K

A

A

L

I

D

D

V

L

V

V

K

K

Q

-

H

-

G

G

F

F

V

E

E

E

active site: N26 (≠ C21), K60 (= K55), D238 (= D243)
binding any 5'-monophosphate nucleotide: P115 (= P110), A116 (= A111), F117 (= F112), K138 (= K133), R168 (= R163), H202 (= H195)

1phqA Crystal structure of kdo8p synthase in its binary complex with substrate analog e-fpep
46% identity, 96% coverage: 7:274/279 of query aligns to 12:267/272 of 1phqA

query
sites
1phqA

H

N

V

V

G

A

I

N

D

D

Q

L

P

P

F

F

F

V

L

L

I

F

A

G

G

G

P

M

C
x
N

V

V

I

L

E

E

S

S

E

R

Q

D

L

L

A

A

I

M

D

R

T

I

A

C

G

E

Q

H

L

Y

K

V

E

T

L

V

T

T

T

Q

R

K

L

L

G

G

I

I

P

P

F

Y

I

V

F

F

K

K

S

A

S

S

Y

F

D

D

K
|
K

A

A

N

N

R

R

S

S

T

I

A

H

S

S

F

Y

R

R

G

G

L

P

G

G

I

L

D

E

E

E

G

G

L

M

R

K

I

I

L

F

Q

Q

K

E

V

L

K

K

D

Q

E

T

I

F

G

G

V

V

P

K

V

I

L

I

T

T

D

D

V

V

H

H

E

E

D

P

T

S

P

Q

L

A

A

Q

E

P

V

V

A

A

S

D

V

V

D

D

V

V

M

I

Q

Q

T

L

P
|
P

A
|
A

F
|
F

L

L

V

A

R

R

Q

Q

T

T

N

D

F

L

I

V

Q

E

N

A

V

M

C

A

R

K

Q

T

G

G

L

A

P

V

V

I

N

N

I

V

K

K

G

P

Q

Q

F

F

Q

V

A

S

P

P

W

G

D

Q

M

M

D

G

Q

N

V

I

V

V

A

D

K

K

A

F

R

K

E

E

V

G

G

G

N

N

E

E

Q

K

I

V

M

I

I

L

C

C

D

D

R
|
R

G

G

T

A

S

N

F

F

G

G

Y

Y

N

D

T

N

L

L

I

V

S

V

D

D

M

M

R

L

G

G

L

F

A

S

S

I

M

M

R

K

T

V

-

S

-

G

G

N

C

S

P

P

V

V

V

I

F

F

D

D

A

V

T

T

H
|
H

S

A

V

L

Q

-

P

-

G

-

Q

-

G

-

S

-

T

-

S

-

G

-

Q

Q

R

R

E

A

F

Q

V

V

P

A

V

E

L

L

A

A

R

R

A

A

A

G

I

M

A

A

A

V

G

G

V

L

A

A

G

G

I

L

F

F

M

I

E

E

T

A

H

H

P

P

D

D

P

P

A

E

N

H

A

A

K

K

S

C

D
|
D

G

G

P

P

N

S

M

A

W

L

P

P

L

L

D

A

Q

K

L

L

E

E

P

P

V

F

L

L

A

K

V

Q

L

M

K

K

A

A

L

I

D

D

V

L

V

V

K

K

Q

-

H

-

G

G

F

F

V

E

E

E

active site: N26 (≠ C21), K60 (= K55), D238 (= D243)
binding 3-fluoro-2-(phosphonooxy)propanoic acid: P115 (= P110), A116 (= A111), F117 (= F112), R168 (= R163), H202 (= H195)

1gg0A Crystal structure analysis of kdop synthase at 3.0 a (see paper)
46% identity, 96% coverage: 7:274/279 of query aligns to 12:270/275 of 1gg0A

query
sites
1gg0A

H

N

V

V

G

A

I

N

D

D

Q

L

P

P

F

F

F

V

L

L

I

F

A

G

G

G

P

M

C
x
N

V

V

I

L

E

E

S

S

E

R

Q

D

L

L

A

A

I

M

D

R

T

I

A

C

G

E

Q

H

L

Y

K

V

E

T

L

V

T

T

T

Q

R

K

L

L

G

G

I

I

P

P

F

Y

I

V

F

F

K

K

S

A

S

S

Y

F

D

D

K
|
K

A

A

N

N

R

R

S

S

T

I

A

H

S

S

F

Y

R

R

G

G

L

P

G

G

I

L

D

E

E

E

G

G

L

M

R

K

I

I

L

F

Q

Q

K

E

V

L

K

K

D

Q

E

T

I

F

G

G

V

V

P

K

V

I

L

I

T

T

D

D

V

V

H

H

E

E

D

P

T

S

P

Q

L

A

A

Q

E

P

V

V

A

A

S

D

V

V

D

D

V

V

M

I

Q

Q

T

L

P

P

A
|
A

F

F

L

L

V

A

R

R

Q

Q

T

T

N

D

F

L

I

V

Q

E

N

A

V

M

C

A

R

K

Q

T

G

G

L

A

P

V

V

I

N

N

I

V

K
|
K

K

K

G

P

Q

Q

F

F

Q

V

A

S

P

P

W

G

D

Q

M

M

D

G

Q

N

V

I

V

V

A

D

K

K

A

F

R

K

E

E

V

G

G

G

N

N

E

E

Q

K

I

V

M

I

I

L

C

C

D

D

R
|
R

G

G

T

A

S

N

F

F

G

G

Y

Y

N

D

T

N

L

L

I

V

S

V

D

D

M

M

R

L

G

G

L

F

A

S

S

I

M

M

R

K

T

V

-

S

-

G

G

N

C

S

P

P

V

V

V

I

F

F

D

D

A

V

T

T

H

H

S

A

V

L

Q

Q

Q

-

P

-

G

-

Q

-

G

-

S

-

T

-

S

-

G

C

G

R

Q

R

R

R

E

A

F

Q

V

V

P

A

V

E

L

L

A

A

R

R

A

A

A

G

I

M

A

A

A

V

G

G

V

L

A

A

G

G

I

L

F

F

M

I

E

E

T

A

H

H

P

P

D

D

P

P

A

E

N

H

A

A

K

K

S

C

D
|
D

G

G

P

P

N

S

M

A

W

L

P

P

L

L

D

A

Q

K

L

L

E

E

P

P

V

F

L

L

A

K

V

Q

L

M

K

K

A

A

L

I

D

D

V

L

V

V

K

K

Q

-

H

-

G

G

F

F

V

E

E

E

active site: N26 (≠ C21), K60 (= K55), D241 (= D243)
binding phosphate ion: A116 (= A111), K138 (= K133), R168 (= R163)

3e12A Cu2+ substituted aquifex aeolicus kdo8ps in complex with kdo8p (see paper)
47% identity, 93% coverage: 12:270/279 of query aligns to 1:254/258 of 3e12A

query
sites
3e12A

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C
|
C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q

Q

Q

L

P

P

G

G

Q

-

G

-

S

-

T

-

S

-

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E
|
E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding copper (ii) ion: C10 (= C21), H184 (= H195), E216 (= E232), D227 (= D243)
binding 3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid: K40 (= K50), K45 (= K55), N47 (= N57), R48 (= R58), S49 (= S59), Q98 (= Q108), K123 (= K133), H184 (= H195), D227 (= D243)
binding phosphate ion: P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163)

1pcwA Aquifex aeolicus kdo8ps in complex with cadmium and app, a bisubstrate inhibitor (see paper)
46% identity, 93% coverage: 12:270/279 of query aligns to 1:253/257 of 1pcwA

query
sites
1pcwA

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K

K

S

S

Y

F

D

D

K
|
K

A

A

N
|
N

R
|
R

S
|
S

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D

D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q

Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V

K
|
K

K

K

G

G

Q

Q

F

F

Q

L

A

A

P

P

W

W

D

D

M

T

D

K

Q

N

V

V

A

E

K

K

A

L

R

K

E

F

V

G

G

G

N

A

E

K

Q

E

I

I

M

Y

I

L

C

T

D

E

R
|
R

G

G

T

T

S

T

F

F

G

G

Y

Y

N

N

T

N

L

L

I

V

S

V

D

D

M

F

R

R

G

S

L

L

A

P

S

I

M

M

R

K

R

Q

T

-

G

W

C

A

P

K

V

V

V

I

F

Y

D

D

A

A

T

T

H
|
H

S

S

V

V

Q
|
Q

Q

L

P

P

G

G

G

-

Q

-

G

-

S

-

T

-

S

-

G

G

Q

M

R

R

E

E

F

F

V

I

P

F

V

P

L

L

A

I

R

R

A

A

I

V

A

A

A

V

G

G

V

C

A

D

G

G

I

V

F

F

M

M

E

E

T

T

H

H

P

P

D

E

P

P

A

E

N

K

A

A

K

L

S

S

D
|
D

G

A

P

S

N

T

M

Q

W

L

P

P

L

L

D

S

Q

Q

L

L

E

E

P

G

V

I

L

I

A

E

V

A

L

I

K

L

A

E

L

I

D

R

D

E

V

V

V

A

K

S

Q

K

H

Y

binding 1-deoxy-6-o-phosphono-1-[(phosphonomethyl)amino]-l-threo-hexitol: K45 (= K55), N47 (= N57), R48 (= R58), S49 (= S59), P100 (= P110), A101 (= A111), K123 (= K133), R153 (= R163), H184 (= H195), Q187 (= Q198), D226 (= D243)

1pe1A Aquifex aeolicus kdo8ps in complex with cadmium and 2-pga (see paper)
46% identity, 93% coverage: 12:270/279 of query aligns to 2:254/258 of 1pe1A

query
sites
1pe1A

Q

E

P

K

F

F

F

L

L

V

I

I

A

A

G

G

P

P

C

C

V

A

I

I

E

E

S

S

E

E

Q

E

L

L

A

L

I

L

D

K

T

V

A

G

G

E

Q

E

L

I

K

K

E

R

L

L

T

S

T

E

R

K

L

F

G

K

-

E

I

V

P

E

F

F

I

V

F

F

K
|
K

S

S

Y

F

D

D

K

K

A

A

N

N

R

R

S

S

T

I

A

H

S

S

F

F

R

R

G

G

L

H

G

G

I

L

D

E

E

Y

G

G

L

V

R

K

I

A

L

L

Q

R

K

K

V

V

K

K

D

E

E

E

I

F

G

G

V

L

P

K

V

I

L

T

T

T

D
|
D

V

I

H

H

E

E

D

S

T

W

P

Q

L

A

A

E

E

P

V

V

A

A

S

E

V

V

V

A

D

D

V

I

M

I

Q
|
Q

T

I

P
|
P

A
|
A

F

F

L

L

V

C

R

R

Q

Q

T

T

N

D

F

L

I

L

Q

L

N

A

V

A

C

A

R

K

Q

T

G

G

L

R

P

A

V

V

N

N

I

V