SitesBLAST

SitesBLAST – Find functional sites

SitesBLAST

Comparing WP_013817575.1 NCBI__GCF_000214665.1:WP_013817575.1 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)

6xxyA Crystal structure of haemophilus influenzae 3-isopropylmalate dehydrogenase in complex with o-isobutenyl oxalylhydroxamate. (see paper)
43% identity, 98% coverage: 1:362/368 of query aligns to 1:358/358 of 6xxyA

query
sites
6xxyA

M

M

K

E

H

S

Y

Y

K

N

I

I

A

A

V

V

L

L

A

A

G

G

D

D

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G

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P

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E

A

A

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E

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F

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E

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Y

A

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C

C

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D

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D

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F

G

G

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x
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x
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G
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L

-

S

-

H

G

E

P

E

K

S

W

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K

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I

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D

K

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Q

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E
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E

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G

G

A

A

L
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L

L

L

P

P

M

L

R

R

R

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R

H

Y

F

N

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T

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Y

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A

C

N

N

F

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R
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R

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x
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I
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I

active site: Y144 (= Y146), K194 (= K196), D226 (= D228), D250 (= D252)
binding magnesium ion: D250 (= D252), D254 (= D256)
binding nicotinamide-adenine-dinucleotide: S74 (≠ P74), V75 (≠ I75), G76 (= G76), E90 (= E92), L94 (= L96), Y224 (≠ L226), N227 (≠ A229), M230 (≠ T232), M263 (≠ L265), G264 (= G266), E280 (= E281), G283 (≠ H284), G284 (= G285), S285 (= S286), A286 (= A287), P287 (= P288), D288 (= D289), I289 (= I290), N296 (= N297), D337 (= D338)
binding 2-(2-methylprop-2-enoxyamino)-2-oxidanylidene-ethanoic acid: E90 (= E92), R108 (= R110), R137 (= R139), K194 (= K196), V197 (= V199), D226 (= D228), D250 (= D252)

1cnzA 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium (see paper)
42% identity, 97% coverage: 2:358/368 of query aligns to 3:355/363 of 1cnzA

query
sites
1cnzA

K

K

H

N

Y

Y

K

H

I

I

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

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T

M

Q

A

E

Q

A

A

L

L

K

K

V

V

L

M

K

D

V

A

I

V

E

R

E

S

R

R

N

F

D

D

V

M

T

R

F

I

E

T

L

T

M

S

P

H

A

Y

L

D

F

V

G

G

A

G

C

I

A

A

Y

I

F

D

E

N

T

H

G

G

D

H

A

P

F

L

P

P

Q

K

A

A

T

T

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V

D

E

I

G

C

C

D

E

Q

Q

A

A

D

D

A

A

I

I

L

L

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F

G

G

P

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V

G

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L

G

S

P

H

K

E

W

E

E

S

N

K

-

K

-

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Q

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P

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E

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G

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A

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L

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Y

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F

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A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

N

I

I

A

A

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N

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P

Y

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I

I

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L

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S

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L

A

A

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L

M

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Y

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D

D

M

A

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A

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T

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A

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Y

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-

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I

active site: Y145 (= Y146), K195 (= K196), D227 (= D228), D251 (= D252)
binding manganese (ii) ion: D251 (= D252), D255 (= D256)

P37412 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
42% identity, 97% coverage: 2:358/368 of query aligns to 3:355/363 of P37412

query
sites
P37412

K

K

H

N

Y

Y

K

H

I

I

A

A

V

V

L

L

A

P

G

G

D

D

G

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I

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P

E

E

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M

Q

A

E

Q

A

A

L

L

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K

V

V

L

M

K

D

V

A

I

V

E

R

E

S

R

R

N

F

D

D

V

M

T

R

F

I

E

T

L

T

M

S

P

H

A

Y

L

D

F

V

G

G

A

G

C

I

A

A

Y

I

F

D

E

N

T

H

G

G

D

H

A

P

F

L

P

P

Q

K

A

A

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T

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E

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C

C

D

E

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Q

A

A

D

D

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A

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F

G

G

P

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G

G

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H

K

E

W

E

E

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N

K

-

K

-

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P

P

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P

D

E

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Q

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P

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E

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R

G

G

A

A

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L

L

L

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P

M

L

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N

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N

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A

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K

D

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Y

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P

D

D

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E

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L

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Y

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D

A

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A

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D

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G

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Y

Y

E

E

P

P

S

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

N

I

I

A

A

N

N

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P

Y

I

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M

Q

I

I

G

L

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L

A

A

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M

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L

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Y

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D

M

A

A

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A

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Y

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D

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-

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E

E

F

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G

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D

K

I

V

I

D227 (= D228) binding Mn(2+)
D251 (= D252) binding Mn(2+)
D255 (= D256) binding Mn(2+)

3vmkA 3-isopropylmalate dehydrogenase from shewanella benthica db21 mt-2 (see paper)
43% identity, 98% coverage: 4:364/368 of query aligns to 9:368/369 of 3vmkA

query
sites
3vmkA

Y

Y

K

Q

I

I

A

A

V

V

L

L

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

T

M

Q

A

E

E

A

A

L

R

K

K

V

V

L

L

K

A

V

A

I

V

E

E

E

K

R

R

N

F

D

D

V

L

T

S

F

I

E

E

L

Y

M

S

P

E

A

Y

L

D

F

V

G

G

A

G

C

A

A

A

Y

I

F

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E

N

T

H

G

G

D

C

A

P

F

L

P

P

Q

E

A

A

T

T

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L

D

K

I

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C

C

D

E

Q

A

A

A

D

D

A

A

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L

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F

G

G

P

S

I

V

G

G

L

G

S

P

H

K

E

W

E

E

S

-

K

-

K

H

I

L

P

P

V

P

D

N

K

D

Q

Q

P

P

E

E

R

R

G

G

A

A

L

L

L

L

P

P

M

L

R
|
R

R

G

R

H

Y

F

N

E

T

L

Y

F

A

C

N

N

F

M

R

R

P

P

V

A

S

K

L

L

P

H

K

P

S

G

L

L

A

E

H

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F

M

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P

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R

P

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D

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I

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E

E

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G

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D

D

L

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C

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V

R
|
R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

-

K

K

E

P

R

K

G

G

V

R

N

Q

D

G

K

E

G

G

L

E

-

N

R

E

Y

E

V

A

R

F

E

D

T

T

L

M

E

R

Y

Y

D

S

E

R

E

K

Q

E

I

I

R

R

R

R

I

I

M

A

H

K

E

I

A

A

F

F

K

E

L

S

A

A

S

Q

K

G

R

R

R

R

K

K

L

K

L

V

H

T

N

S

I

V

H

D

K
|
K

S

A

N
|
N

V

V

L

L

M

A

S

C

S

S

V

V

L

L

W

W

N

R

E

E

V

V

M

V

E

E

E

E

V

V

A

A

K

K

D

D

Y

Y

P

P

D

D

V

V

E

E

V

L

V

E

N

H

Y

I

L

Y

V

I

D
|
D

A

N

A

A

A

T

T

M

A

Q

L

L

C

L

L

R

K

R

P

P

T

N

Q

E

F

F

D

D

V

V

M

M

V

L

M

C

E

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

V

S

S

D
|
D

Q

E

G

I

G

A

G

M

V

L

L

T

G

G

S

S

L

M

G

G

L

L

M

L

P

A

S

S

A

I

C

S

I

M

G

N

P

S

E

Q

K

G

-

F

A

G

Y

M

Y

Y

E

E

P

P

S

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

N

G

I

I

A

A

N

N

P

P

Y

V

S

A

M

Q

I

I

G

L

S

S

V

A

A

A

M

L

M

L

L

L

E

R

N

H

S

S

F

L

D

K

M

L

A

E

A

D

E

A

A

A

K

L

N

A

V

I

W

E

A

A

A

A

M

V

Q

S

G

K

V

A

F

L

A

S

D

D

G

G

Y

Y

S

L

T

T

A

C

D

E

L

L

S

L

K

P

P

A

G

S

S

E

G

R

V

S

T

Q

M

A

I

K

S

S

T

T

V

S

E

Q

F

M

G

G

D

D

K

Y

V

I

V

A

E

Q

K

A

L

I

R

A

Q

E

active site: Y149 (= Y146), K199 (= K196), D231 (= D228), D255 (= D252), D259 (= D256)
binding 3-isopropylmalic acid: R103 (= R100), R142 (= R139), Y149 (= Y146), K199 (= K196), N201 (= N198), D255 (= D252)

1a05A Crystal structure of the complex of 3-isopropylmalate dehydrogenase from thiobacillus ferrooxidans with 3-isopropylmalate (see paper)
44% identity, 97% coverage: 5:362/368 of query aligns to 3:354/357 of 1a05A

query
sites
1a05A

K

K

I

I

A

A

V

I

L

F

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

T

V

Q

A

E

A

A

A

L

R

K

Q

V

V

L

L

K

D

V

A

I

V

E

D

E

Q

R

A

N

A

D

H

V

L

T

G

F

L

E

R

L

C

M

T

P

E

A

G

L

L

F

V

G

G

A

G

C

A

A

A

Y

L

F

D

E

A

T

S

G

D

D

D

A

P

F

L

P

P

Q

A

A

A

T

S

I

L

D

Q

I

L

C

A

D

M

Q

A

A

A

D

D

A

A

I

V

L

I

K

L

G

G

P

A

I

V

G

G

L

G

S

P

H

R

E

W

E

D

S

A

K

-

K

-

I

Y

P

P

V

P

D

A

K

K

Q

R

P

P

E

E

R

Q

G

G

A

-

L

L

L

L

P

R

M

L

R
|
R

R

K

R

G

Y

L

N

D

T

L

Y

Y

A

A

N

N

F

L

R
|
R

P

P

V

A

S

Q

L

I

P

F

K

P

S

Q

L

L

A

L

H

D

F

A

S

S

P

P

L

L

K

R

P

P

E

E

I

L

I

V

G

R

E

D

G

-

I

V

D

D

L

I

I

L

M

V

V

V

R
|
R

E

E

L

L

V

T

G

G

G

D

L

I

Y
|
Y

F

F

G

G

N

-

K

Q

E

P

R

R

G

G

V

L

N

E

-

V

D

I

K

D

G

G

L

K

R

R

Y

R

V

G

R

F

E

N

T

T

L

M

E

V

Y

Y

D

D

E

E

E

D

Q

E

I

I

R

R

R

R

I

I

M

A

H

H

E

V

A

A

F

F

K

R

L

A

A

A

S

Q

K

G

R

R

R

R

K

K

L

Q

L

L

H

C

N

S

I

V

H

D

K
|
K

S

A

N

N

V

V

L

L

M

E

S

T

S

T

V

R

L

L

W

W

N

R

E

E

V

V

M

V

E

T

E

E

V

V

A

A

K

R

D

D

Y

Y

P

P

D

D

V

V

E

R

V

L

V

S

N

H

Y

M

L

Y

V

V

D
|
D

A

N

A

A

A

A

T

M

A

Q

L

L

C

I

L

R

K

A

P

P

T

A

Q

Q

F

F

D

D

V

V

M

L

V

L

M

T

E

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

E

G

A

G

S

G

Q

V

L

L

T

G

G

S

S

L

I

G

G

L

M

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

E

E

G

K

R

A

A

Y

M

Y

Y

E

E

P

P

S

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

N

D

I

K

A

A

N

N

P

P

Y

L

S

A

M

T

I

I

G

L

S

S

V

V

A

A

M

M

M

M

L

L

E

R

N

H

S

S

F

L

D

N

M

A

A

E

A

P

E

W

A

A

K

Q

N

R

V

V

W

E

A

A

A

A

M

V

Q

Q

G

R

V

V

F

L

A

D

D

Q

G

G

Y

L

S

R

T

T

A

A

D

D

L

I

S

A

K

A

P

P

G

G

S

T

G

P

V

V

T

-

M

-

I

I

S

G

T

T

V

K

E

A

F

M

G

G

D

A

K

A

V

V

V

V

E

N

K

A

L

L

active site: Y140 (= Y146), K190 (= K196), D222 (= D228), D246 (= D252), D250 (= D256)
binding 3-isopropylmalic acid: R95 (= R100), R105 (= R110), R133 (= R139), Y140 (= Y146), D246 (= D252)

Q56268 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Acidithiobacillus ferrooxidans (Thiobacillus ferrooxidans) (see paper)
44% identity, 97% coverage: 5:362/368 of query aligns to 3:354/358 of Q56268

query
sites
Q56268

K

K

I

I

A

A

V

I

L

F

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

T

V

Q

A

E

A

A

A

L

R

K

Q

V

V

L

L

K

D

V

A

I

V

E

D

E

Q

R

A

N

A

D

H

V

L

T

G

F

L

E

R

L

C

M

T

P

E

A

G

L

L

F

V

G

G

A

G

C

A

A

A

Y

L

F

D

E

A

T

S

G

D

D

D

A

P

F

L

P

P

Q

A

A

A

T

S

I

L

D

Q

I

L

C

A

D

M

Q

A

A

A

D

D

A

A

I

V

L

I

K

L

G

G

P

A

I

V

G

G

L

G

S

P

H

R

E

W

E

D

S

A

K

-

K

-

I

Y

P

P

V

P

D

A

K

K

Q

R

P

P

E

E

R

Q

G

G

A

-

L

L

L

L

P

R

M

L

R
|
R

R

K

R

G

Y

L

N

D

T

L

Y

Y

A

A

N

N

F

L

R
|
R

P

P

V

A

S

Q

L

I

P

F

K

P

S

Q

L

L

A

L

H

D

F

A

S

S

P

P

L

L

K

R

P

P

E

E

I

L

I

V

G

R

E

D

G

-

I

V

D

D

L

I

I

L

M

V

V

V

R
|
R

E

E

L

L

V

T

G

G

G

D

L

I

Y

Y

F

F

G

G

N

-

K

Q

E

P

R

R

G

G

V

L

N

E

-

V

D

I

K

D

G

G

L

K

R

R

Y

R

V

G

R

F

E

N

T

T

L

M

E

V

Y

Y

D

D

E

E

E

D

Q

E

I

I

R

R

R

R

I

I

M

A

H

H

E

V

A

A

F

F

K

R

L

A

A

A

S

Q

K

G

R

R

R

R

K

K

L

Q

L

L

H

C

N

S

I

V

H

D

K

K

S

A

N

N

V

V

L

L

M

E

S

T

S

T

V

R

L

L

W

W

N

R

E

E

V

V

M

V

E

T

E

E

V

V

A

A

K

R

D

D

Y

Y

P

P

D

D

V

V

E

R

V

L

V

S

N

H

Y

M

L

Y

V

V

D
|
D

A

N

A

A

A

A

T

M

A

Q

L

L

C

I

L

R

K

A

P

P

T

A

Q

Q

F

F

D

D

V

V

M

L

V

L

M

T

E

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D

D

Q

E

G

A

G

S

G

Q

V

L

L

T

G

G

S

S

L

I

G

G

L

M

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

E

E

G

K

R

A

A

Y

M

Y

Y

E

E

P

P

S

I

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

Q

N

D

I

K

A

A

N

N

P

P

Y

L

S

A

M

T

I

I

G

L

S

S

V

V

A

A

M

M

M

M

L

L

E

R

N

H

S

S

F

L

D

N

M

A

A

E

A

P

E

W

A

A

K

Q

N

R

V

V

W

E

A

A

A

A

M

V

Q

Q

G

R

V

V

F

L

A

D

D

Q

G

G

Y

L

S

R

T

T

A

A

D

D

L

I

S

A

K

A

P

P

G

G

S

T

G

P

V

V

T

-

M

-

I

I

S

G

T

T

V

K

E

A

F

M

G

G

D

A

K

A

V

V

V

V

E

N

K

A

L

L

R95 (= R100) binding substrate
R105 (= R110) binding substrate
R133 (= R139) binding substrate
D222 (= D228) binding Mg(2+); binding substrate
D246 (= D252) binding Mg(2+)

4xxvA Crystal structure of 3-isopropylmalate dehydrogenase from burkholderia thailandensis in complex with NAD
45% identity, 98% coverage: 3:362/368 of query aligns to 1:356/356 of 4xxvA

query
sites
4xxvA

H

H

Y

M

K

K

I

I

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

T

V

Q

N

E

E

A

A

L

V

K

K

V

V

L

L

K

N

V

A

I

L

E

D

E

E

R

K

N

-

D

-

V

-

T

-

F

F

E

E

L

L

M

E

P

H

A

A

L

P

F

V

G

G

A

G

C

A

A

G

Y

Y

F

E

E

A

T

S

G

G

D

H

A

P

F

L

P

P

Q

D

A

A

T

T

I

L

D

A

I

L

C

A

D

K

Q

E

A

A

D

D

A

A

I

I

L

L

K

F

G

G

P

A

I

V

G

G

L

D

S

W

H

K

E

Y

E

D

S

S

K

L

K

E

I

R

P

A

V

L

D

-

K

-

Q

R

P

P

E

E

R

Q

G

-

A

A

L

I

L

L

P

G

M

L

R

R

R

K

R

H

Y

L

N

E

T

L

Y

F

A

A

N

N

F

F

R

R

P

P

V

A

S

I

L

C

P

Y

K

P

S

Q

L

L

A

V

H

D

F

A

S

S

P

P

L

L

K

K

P

P

E

E

I

L

I

V

G

A

E

-

G

G

I

L

D

D

L

I

I

L

M

I

V

V

R

R

E

E

L

L

V

N

G

G

G

D

L

I

Y
|
Y

F

F

G

G

N

-

K

Q

E

P

R

R

G

G

V

V

N

R

D

A

K

A

-

P

-

D

-

G

-

P

-

F

-

A

G

G

L

E

R

R

Y

E

V

G

R

F

E

D

T

T

L

M

E

R

Y

Y

D

S

E

E

E

P

Q

E

I

V

R

R

R

R

I

I

M

A

H

H

E

V

A

A

F

F

K

Q

L

A

A

A

S

Q

K

K

R

R

R

A

K

K

L

K

L

L

H

L

N

S

I

V

H

D

K
|
K

S

S

N
|
N

V

V

L

L

M

E

S

T

S

S

V

Q

L

F

W

W

N

R

E

D

V

V

M

M

E

I

E

D

V

V

A

S

K

K

D

E

Y

Y

P

A

D

D

V

V

E

E

V

L

V

S

N

H

Y

M

L
x
Y

V

V

D
|
D

A
x
N

A

A

A

A

T

M

A

Q

L

L

C

A

L

K

K

A

P

P

T

K

Q

Q

F

F

D

D

V

V

M

I

V

V

M

T

E

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

E

G

A

G

S

G

M

V

L

L

T

G

G

S

S

L

I

G

G

L

M

M

L

P

P

S

S

A

A

C

S

I

L

G

D

P

K

-

N

E

N

K

K

A

G

Y

L

Y

Y

E

E

P

P

S

S

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

G

I

I

A

A

N

N

P

P

Y

L

S

A

M

T

I

I

G

L

S

S

V

A

A

A

M

M

M

L

L

L

E

R

N

Y

S

S

F

L

D

N

M

R

A

A

A

E

E

Q

A

A

K

D

N

R

V

I

W

E

A

R

A

A

M

V

Q

K

G

T

V

V

F

L

A

E

D

Q

G

G

Y

Y

S

R

T

T

A

G

D

D

L

I

S

A

K

T

P

P

G

-

S

-

G

G

V

C

T

R

M

Q

I

V

S

G

T

T

V

A

E

A

F

M

G

G

D

D

K

A

V

V

V

V

E

A

K

A

L

L

active site: Y136 (= Y146), K191 (= K196), D223 (= D228), D247 (= D252), D251 (= D256)
binding nicotinamide-adenine-dinucleotide: N193 (= N198), Y221 (≠ L226), N224 (≠ A229)

4iwhA Crystal structure of a 3-isopropylmalate dehydrogenase from burkholderia pseudomallei
45% identity, 98% coverage: 3:362/368 of query aligns to 3:358/358 of 4iwhA

query
sites
4iwhA

H

H

Y

M

K

K

I

I

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

I

T

V

Q

N

E

E

A

A

L

V

K

K

V

V

L

L

K

N

V

A

I

L

E

D

E

E

R

K

N

-

D

-

V

-

T

-

F

F

E

E

L

L

M

E

P

H

A

A

L

P

F

V

G

G

A

G

C

A

A

G

Y

Y

F

E

E

A

T

S

G

G

D

H

A

P

F

L

P

P

Q

D

A

A

T

T

I

L

D

A

I

L

C

A

D

K

Q

E

A

A

D

D

A

A

I

I

L

L

K

F

G

G

P

A

I

V

G

G

L

D

S

W

H

K

E

Y

E

D

S

S

K

L

K

E

I

R

P

A

V

L

D

-

K

-

Q

R

P

P

E

E

R

Q

G

-

A

A

L

I

L

L

P

G

M

L

R

R

R

K

R

H

Y

L

N

E

T

L

Y

F

A

A

N

N

F

F

R

R

P

P

V

A

S

I

L

C

P

Y

K

P

S

Q

L

L

A

V

H

D

F

A

S

S

P

P

L

L

K

K

P

P

E

E

I

L

I

V

G

A

E

-

G

G

I

L

D

D

L

I

I

L

M

I

V

V

R

R

E

E

L

L

V

N

G

G

G

D

L

I

Y
|
Y

F

F

G

G

N

-

K

Q

E

P

R

R

G

G

V

V

N

R

D

A

K

A

-

P

-

D

-

G

-

P

-

F

-

A

G

G

L

E

R

R

Y

E

V

G

R

F

E

D

T

T

L

M

E

R

Y

Y

D

S

E

E

E

P

Q

E

I

V

R

R

R

R

I

I

M

A

H

H

E

V

A

A

F

F

K

Q

L

A

A

A

S

Q

K

K

R

R

R

A

K

K

L

K

L

L

H

L

N

S

I

V

H

D

K
|
K

S

S

N

N

V

V

L

L

M

E

S

T

S

S

V

Q

L

F

W

W

N

R

E

D

V

V

M

M

E

I

E

D

V

V

A

S

K

K

D

E

Y

Y

P

A

D

D

V

V

E

E

V

L

V

S

N

H

Y

M

L

Y

V

V

D
|
D

A

N

A

A

A

A

T

M

A

Q

L

L

C

A

L

K

K

A

P

P

T

K

Q

Q

F

F

D

D

V

V

M

I

V

V

M

T

E

G

N

N

M

M

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

E

G

A

G

S

G

M

V

L

L

T

G

G

S

S

L

I

G

G

L

M

M

L

P

P

S

S

A

A

C

S

I

L

G

D

P

K

-

N

E

N

K

K

A

G

Y

L

Y

Y

E

E

P

P

S

S

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

G

I

I

A

A

N

N

P

P

Y

L

S

A

M

T

I

I

G

L

S

S

V

A

A

A

M

M

M

L

L

L

E

R

N

Y

S

S

F

L

D

N

M

R

A

A

A

E

E

Q

A

A

K

D

N

R

V

I

W

E

A

R

A

A

M

V

Q

K

G

T

V

V

F

L

A

E

D

Q

G

G

Y

Y

S

R

T

T

A

G

D

D

L

I

S

A

K

T

P

P

G

-

S

-

G

G

V

C

T

R

M

Q

I

V

S

G

T

T

V

A

E

A

F

M

G

G

D

D

K

A

V

V

V

V

E

A

K

A

L

L

active site: Y138 (= Y146), K193 (= K196), D225 (= D228), D249 (= D252), D253 (= D256)
binding magnesium ion: D249 (= D252), D253 (= D256)

3vkzA 3-isopropylmalate dehydrogenase from shewanella oneidensis mr-1 at atmospheric pressure (see paper)
43% identity, 98% coverage: 4:363/368 of query aligns to 3:361/364 of 3vkzA

query
sites
3vkzA

Y

Y

K

Q

I

I

A

A

V

V

L

L

A

A

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

T

M

Q

A

E

E

A

A

L

R

K

K

V

V

L

L

K

K

V

A

I

V

E

E

E

A

R

R

N

F

D

G

V

L

T

N

F

I

E

E

L

Y

M

T

P

E

A

Y

L

D

F

V

G

G

A

G

C

I

A

A

Y

I

F

D

E

N

T

H

G

G

D

C

A

P

F

L

P

P

Q

E

A

A

T

T

I

L

D

K

I

G

C

C

D

E

Q

A

A

A

D

D

A

A

I

I

L

L

K

F

G

G

P

S

I

V

G

G

L

G

S

P

H

K

E

W

E

E

S

-

K

-

K

K

I

L

P

P

V

P

D

N

K

E

Q

Q

P

P

E

E

R

R

G

G

A

A

L

L

L

L

P

P

M

L

R
|
R

R

G

R

H

Y

F

N

E

T

L

Y

F

A

C

N

N

F

L

R

R

P

P

V

A

S

K

L

L

P

H

K

D

S

G

L

L

A

E

H

H

F

M

S

S

P

P

L

L

K

R

P

S

E

D

I

I

I

S

G

A

E

R

G

G

I

F

D

D

L

V

I

L

M

C

V

V

R
|
R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

-

K

K

E

P

R

K

G

G

V

R

N

Q

D

G

K

E

G

G

-

E

L

S

R

E

Y

E

V

A

R

F

E

D

T

T

L

M

E

R

Y

Y

D

S

E

R

E

R

Q

E

I

I

R

S

R

R

I

I

M

A

H

R

E

I

A

A

F

F

K

E

L

A

A

A

S

R

K

G

R

R

R

R

K

K

L

K

L

V

H

T

N

S

I

V

H

D

K
|
K

S

A

N

N

V

V

L

L

M

A

S

C

S

S

V

V

L

L

W

W

N

R

E

Q

V

V

M

V

E

E

E

E

V

V

A

A

K

V

D

D

Y

F

P

P

D

D

V

V

E

E

V

L

V

E

N

H

Y

I

L

Y

V

I

D
|
D

A

N

A

A

A

T

T

M

A

Q

L

L

C

L

L

R

K

R

P

P

T

D

Q

E

F

F

D

D

V

V

M

M

V

L

M

C

E

S

N

N

M

L

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

E

G

I

G

A

G

M

V

L

L

T

G

G

S

S

L

M

G

G

L

L

M

L

P

S

S

S

A

A

C

S

I

M

G

N

P

S

E

T

K

G

-

F

A

G

Y

L

Y

F

E

E

P

P

S

A

H

G

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

G

I

I

A

A

N

N

P

P

Y

I

S

A

M

Q

I

I

G

L

S

S

V

A

A

A

M

L

M

M

L

L

E

R

N

H

S

S

F

L

D

K

M

Q

A

E

A

E

E

A

A

A

K

S

N

A

V

I

W

E

A

R

A

A

M

V

Q

T

G

K

V

A

F

L

A

N

D

S

G

G

Y

Y

S

L

T

T

A

G

D

E

L

L

S

L

K

S

P

S

G

D

S

Q

G

R

V

H

T

K

M

A

I

K

S

T

T

T

V

V

E

Q

F

M

G

G

D

D

K

F

V

I

V

A

E

D

K

A

L

V

R

K

active site: Y143 (= Y146), K193 (= K196), D225 (= D228), D249 (= D252), D253 (= D256)
binding calcium ion: D249 (= D252), D253 (= D256)
binding 3-isopropylmalic acid: R97 (= R100), R136 (= R139), Y143 (= Y146), D249 (= D252)

2y42D Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with nadh and mn (see paper)
43% identity, 86% coverage: 5:322/368 of query aligns to 3:312/355 of 2y42D

query
sites
2y42D

K

K

I

V

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

T

T

Q

E

E

A

A

A

L

L

K

K

V

V

L

L

K

R

V

A

I

L

E

D

E

E

R

A

N

E

D

G

V

L

-

G

-

L

T

A

F

Y

E

E

L

V

M

F

P

P

A

-

L

-

F

F

G

G

A

G

C

A

A

A

Y

I

F

D

E

A

T

F

G

G

D

E

A

P

F

F

P

P

Q

E

A

P

T

T

I

R

D

K

I

G

C

V

D

E

Q

E

A

A

D

E

A

A

I

V

L

L

K

L

G

G

P

S

I

V

G

G

L

G

S

P

H

K

E

W

E
x
D

S

G

K

-

K

-

I

L

P

P

V

R

D

K

K

I

Q

R

P

P

E

E

R

T

G

G

A

-

L

L

L

L

P

S

M

L

R

R

R

K

R

S

Y

Q

N

D

T

L

Y

F

A

A

N

N

F

L

R

R

P

P

V

A

S

K

L

V

P

F

K

P

S

G

L

L

A

E

H

R

F

L

S

S

P

P

L

L

K

K

P

E

E

E

I

I

I

-

G

A

E

R

G

G

I

V

D

D

L

V

I

L

M

I

V

V

R

R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

E

K

P

E

-

R

R

G

G

V

M

N

S

D

E

K

A

G

-

L

-

R

-

Y

E

V

A

R

W

E

N

T

T

L

E

E

R

Y

Y

D

S

E

K

E

P

Q

E

I

V

R

E

R

R

I

V

M

A

H

R

E

V

A

A

F

F

K

E

L

A

A

A

S

R

K

K

R

R

R

R

K

K

L

H

L

V

H

V

N

S

I

V

H

D

K
|
K

S

A

N

N

V

V

L

L

M

E

S

V

S

G

V

E

L

F

W

W

N

R

E

K

V

T

M

V

E

E

E

E

V

V

A

G

K

R

D

G

Y

Y

P

P

D

D

V

V

E

A

V

L

V

E

N

H

Y

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

T

M

A

H

L

L

C

V

L

R

K

S

P

P

T

A

Q

R

F

F

D

D

V

V

M

V

V

V

M

T

E

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

L

G

A

G

S

G

V

V

L

L

P

G

G

S

S

L

L

G

G

L

L

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

R

E

G

K

T

A

P

Y

V

Y

F

E

E

P

P

S

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

N

G

I

I

A

A

N
|
N

P

P

Y

T

S

A

M

A

I

I

G

L

S

S

V

A

A

A

M

M

M

M

L

L

E

E

N

H

S

A

F

F

D

G

M

L

A

V

A

E

E

L

A

A

K

R

N

K

V

V

active site: Y140 (= Y146), K186 (= K196), D218 (= D228), D242 (= D252), D246 (= D256)
binding manganese (ii) ion: D242 (= D252), D246 (= D256)
binding nicotinamide-adenine-dinucleotide: I12 (= I14), D79 (≠ E81), H274 (= H284), G275 (= G285), A277 (= A287), D279 (= D289), I280 (= I290), N287 (= N297)

2y41A Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn (see paper)
43% identity, 86% coverage: 5:322/368 of query aligns to 3:312/346 of 2y41A

query
sites
2y41A

K

K

I

V

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

T

T

Q

E

E

A

A

A

L

L

K

K

V

V

L

L

K

R

V

A

I

L

E

D

E

E

R

A

N

E

D

G

V

L

-

G

-

L

T

A

F

Y

E

E

L

V

M

F

P

P

A

-

L

-

F

F

G

G

A

G

C

A

A

A

Y

I

F

D

E

A

T

F

G

G

D

E

A

P

F

F

P

P

Q

E

A

P

T

T

I

R

D

K

I

G

C

V

D

E

Q

E

A

A

D

E

A

A

I

V

L

L

K

L

G

G

P

S

I

V

G

G

L

G

S

P

H

K

E

W

E

D

S

G

K

-

K

-

I

L

P

P

V

R

D

K

K

I

Q

R

P

P

E

E

R

T

G

G

A

-

L

L

L

L

P

S

M

L

R
|
R

R

K

R

S

Y

Q

N

D

T

L

Y

F

A

A

N

N

F

L

R
|
R

P

P

V

A

S

K

L

V

P

F

K

P

S

G

L

L

A

E

H

R

F

L

S

S

P

P

L

L

K

K

P

E

E

E

I

I

I

-

G

A

E

R

G

G

I

V

D

D

L

V

I

L

M

I

V

V

R
|
R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

E

K

P

E

-

R

R

G

G

V

M

N

S

D

E

K

A

G

-

L

-

R

-

Y

E

V

A

R

W

E

N

T

T

L

E

E

R

Y

Y

D

S

E

K

E

P

Q

E

I

V

R

E

R

R

I

V

M

A

H

R

E

V

A

A

F

F

K

E

L

A

A

A

S

R

K

K

R

R

R

R

K

K

L

H

L

V

H

V

N

S

I

V

H

D

K
|
K

S

A

N

N

V

V

L

L

M

E

S

V

S

G

V

E

L

F

W

W

N

R

E

K

V

T

M

V

E

E

E

E

V

V

A

G

K

R

D

G

Y

Y

P

P

D

D

V

V

E

A

V

L

V

E

N

H

Y

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

T

M

A

H

L

L

C

V

L

R

K

S

P

P

T

A

Q

R

F

F

D

D

V

V

M

V

V

V

M

T

E

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

L

G

A

G

S

G

V

V

L

L

P

G

G

S

S

L

L

G

G

L

L

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

R

E

G

K

T

A

P

Y

V

Y

F

E

E

P

P

S

V

H

H

G

G

S

S

A

A

P

P

D

D

I

I

A

A

G

G

K

K

N

G

I

I

A

A

N

N

P

P

Y

T

S

A

M

A

I

I

G

L

S

S

V

A

A

A

M

M

M

M

L

L

E

E

N

H

S

A

F

F

D

G

M

L

A

V

A

E

E

L

A

A

K

R

N

K

V

V

active site: Y140 (= Y146), K186 (= K196), D218 (= D228), D242 (= D252), D246 (= D256)
binding 3-isopropylmalic acid: R95 (= R100), R105 (= R110), R133 (= R139), Y140 (= Y146), D242 (= D252)

2ztwA Structure of 3-isopropylmalate dehydrogenase in complex with the inhibitor and NAD+ (see paper)
43% identity, 86% coverage: 5:322/368 of query aligns to 2:311/345 of 2ztwA

query
sites
2ztwA

K

K

I

V

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I
|
I

G

G

P

P

E

E

I

V

T

T

Q

E

E

A

A

A

L

L

K

K

V

V

L

L

K

R

V

A

I

L

E

D

E

E

R

A

N

E

D

G

V

L

-

G

-

L

T

A

F

Y

E

E

L

V

M

F

P

P

A

-

L

-

F

F

G

G

A

G

C

A

A

A

Y

I

F

D

E

A

T

F

G

G

D

E

A

P

F

F

P

P

Q

E

A

P

T

T

I

R

D

K

I

G

C

V

D

E

Q

E

A

A

D

E

A

A

I

V

L

L

K

L

G

G

P

S

I

V

G

G

L

G

S

P

H

K

E

W

E

D

S

G

K

-

K

-

I

L

P

P

V

R

D

K

K

I

Q

R

P

P

E

E

R

T

G

G

A

-

L

L

L

L

P

S

M

L

R

R

R

K

R

S

Y

Q

N

D

T

L

Y

F

A

A

N

N

F

L

R

R

P

P

V

A

S

K

L

V

P

F

K

P

S

G

L

L

A

E

H

R

F

L

S

S

P

P

L

L

K

K

P

E

E

E

I

I

I

-

G

A

E

R

G

G

I

V

D

D

L

V

I

L

M

I

V

V

R

R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

E

K

P

E

-

R

R

G

G

V

M

N

S

D

E

K

A

G

-

L

-

R

-

Y

E

V

A

R

W

E

N

T

T

L

E

E

R

Y

Y

D

S

E

K

E

P

Q

E

I

V

R

E

R

R

I

V

M

A

H

R

E

V

A

A

F

F

K

E

L

A

A

A

S

R

K

K

R

R

R

R

K

K

L

H

L

V

H

V

N

S

I

V

H

D

K
|
K

S

A

N

N

V

V

L

L

M

E

S

V

S

G

V

E

L

F

W

W

N

R

E

K

V

T

M

V

E

E

E

E

V

V

A
x
G

K

R

D

G

Y
|
Y

P

P

D

D

V
|
V

E

A

V

L

V

E

N

H

Y

Q

L

Y

V

V

D
|
D

A

A

A

M

A

A

T

M

A

H

L

L

C

V

L

R

K

S

P

P

T

A

Q

R

F

F

D

D

V

V

M

V

V

V

M

T

E

G

N

N

M

I

F

F

G

G

D
|
D

I

I

L

L

S

S

D
|
D

Q

L

G

A

G

S

G

V

V

L

L

P

G

G

S

S

L

L

G

G

L

L

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

R

E

G

K

T

A

P

Y

V

Y

F

E

E

P

P

S

V

H
|
H

G
|
G

S

S

A
|
A

P

P

D
|
D

I
|
I

A

A

G

G

K

K

N

G

I

I

A
|
A

N
|
N

P

P

Y

T

S

A

M

A

I

I

G

L

S

S

V

A

A

A

M

M

M

M

L

L

E

E

N

H

S

A

F

F

D

G

M

L

A

V

A

E

E

L

A

A

K

R

N

K

V

V

active site: Y139 (= Y146), K185 (= K196), D217 (= D228), D241 (= D252), D245 (= D256)
binding magnesium ion: G203 (≠ A214), Y206 (= Y217), V209 (= V220)
binding nicotinamide-adenine-dinucleotide: I11 (= I14), H273 (= H284), G274 (= G285), A276 (= A287), D278 (= D289), I279 (= I290), A285 (= A296), N286 (= N297)

Q5SIY4 3-isopropylmalate dehydrogenase; 3-IPM-DH; Beta-IPM dehydrogenase; IMDH; EC 1.1.1.85 from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (see 2 papers)
43% identity, 86% coverage: 5:322/368 of query aligns to 2:311/345 of Q5SIY4

query
sites
Q5SIY4

K

K

I

V

A

A

V

V

L

L

A

P

G

G

D

D

G

G

I

I

G

G

P

P

E

E

I

V

T

T

Q

E

E

A

A

A

L

L

K

K

V

V

L

L

K

R

V

A

I

L

E

D

E

E

R

A

N

E

D

G

V

L

-

G

-

L

T

A

F

Y

E

E

L

V

M

F

P

P

A

-

L

-

F

F

G

G

A

G

C

A

A

A

Y

I

F

D

E

A

T

F

G

G

D

E

A

P

F

F

P

P

Q

E

A

P

T

T

I

R

D

K

I

G

C

V

D

E

Q

E

A

A

D

E

A

A

I

V

L

L

K

L

G

G

P

S

I

V

G

G

L
x
G

S
x
P

H
x
K

E
x
W

E
x
D

S
x
G

K

-

K

-

I
x
L

P
|
P

V
x
R

D
x
K

K
x
I

Q
x
R

P
|
P

E
|
E

R

T

G

G

A

-

L

L

L

L

P

S

M

L

R

R

R

K

R

S

Y

Q

N

D

T

L

Y

F

A

A

N

N

F

L

R

R

P

P

V

A

S

K

L

V

P

F

K

P

S

G

L

L

A

E

H

R

F

L

S

S

P

P

L

L

K

K

P

E

E

E

I

I

I

-

G

A

E

R

G

G

I

V

D

D

L

V

I

L

M

I

V

V

R

R

E

E

L

L

V

T

G

G

G

G

L

I

Y
|
Y

F

F

G

G

N

E

K

P

E

-

R

R

G

G

V

M

N

S

D

E

K

A

G

-

L

-

R

-

Y

E

V

A

R

W

E

N

T

T

L

E

E

R

Y

Y

D

S

E

K

E

P

Q

E

I

V

R

E

R

R

I

V

M

A

H

R

E

V

A

A

F

F

K

E

L

A

A

A

S

R

K

K

R

R

R

R

K

K

L

H

L

V

H

V

N

S

I

V

H

D

K

K

S

A

N

N

V

V

L

L

M

E

S

V

S

G

V

E

L

F

W

W

N

R

E

K

V

T

M

V

E

E

E

E

V

V

A

G

K

R

D

G

Y

Y

P

P

D

D

V

V

E

A

V

L

V

E

N

H

Y

Q

L

Y

V

V

D

D

A

A

A

M

A

A

T

M

A

H

L

L

C

V

L

R

K

S

P

P

T

A

Q

R

F

F

D

D

V

V

M

V

V

V

M

T

E

G

N

N

M

I

F

F

G

G

D

D

I

I

L

L

S

S

D

D

Q

L

G

A

G

S

G

V

V

L

L

P

G

G

S

S

L

L

G

G

L

L

M

L

P

P

S

S

A

A

C

S

I

L

G

G

P

R

E

G

K

T

A

P

Y

V

Y

F

E

E

P

P

S

V

H

H

G
|
G

S
|
S

A
|
A

P
|
P

D
|
D

I
|
I

A
|
A

G
|
G

K
|
K

N
x
G

I
|
I