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DCIP_AZOBR_2_545_catalytic

Indole-3-pyruvate decarboxylase [TPP enzyme family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DCIP_AZOBR):R: Thiamine pyrophosphate binding (382, 402:404, 428:431, 434, 456, 458:460)
282:284, 380, 381, 461, 462, 465, 532, 536
282:284, 380:382, 402:404, 428:431, 434, 456, 458:462, 465, 532, 536
A2 (DCIP_AZOBR):22:25, 48, 71, 74, 75, 112, 11322:25, 48, 71, 74, 75, 112, 113
Metals (Me):Mg

Full PDB list

2nxw, 2q5j, 2q5l, 2q5o, 2q5q

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
D
2
8
2
T
2
8
3
M
3
8
0
G
3
8
1
D
3
8
2
A
4
0
2
G
4
0
3
M
4
0
4
G
4
2
8
D
4
2
9
G
4
3
0
A
4
3
1
M
4
3
4
N
4
5
6
S
4
5
8
W
4
5
9
E
4
6
0
M
4
6
1
L
4
6
2
F
4
6
5
F
5
3
2
Q
5
3
6
I
2
2
P
2
3
G
2
4
D
2
5
E
4
8
T
7
1
A
7
4
H
1
1
2
H
1
1
3
[1]2nxw.a tpp26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]2q5j.a tpw26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]2q5l.a r1t,s1t58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]2q5o.a ppy,tpw38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2q5q.a kpv,tpw40 . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . Mg

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1 A2 Me
D
2
8
2
T
2
8
3
N
2
8
4
M
3
8
0
G
3
8
1
D
3
8
2
A
4
0
2
G
4
0
3
M
4
0
4
G
4
2
8
D
4
2
9
G
4
3
0
A
4
3
1
M
4
3
4
N
4
5
6
S
4
5
8
W
4
5
9
E
4
6
0
M
4
6
1
L
4
6
2
F
4
6
5
F
5
3
2
Q
5
3
6
I
2
2
P
2
3
G
2
4
D
2
5
E
4
8
T
7
1
A
7
4
G
7
5
H
1
1
2
H
1
1
3
[1]2nxw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]2q5j.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . - - Mg
[1]2q5l.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Mg
[1]2q5o.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2q5q.a . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . Mg

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2nxw.a:tpp
2q5j.a:tpw
2q5l.a:r1t,s1t
2q5o.a:ppy,tpw
2q5q.a:kpv,tpw
[1] 2nxw.a
0.1
0.1 0.1 0.6 0.3
[1] 2q5j.a 0.1
0.2
0.7 2.0 1.7
[1] 2q5l.a 0.1 0.2
0.1
1.4 0.7
[1] 2q5o.a 0.1 0 0.2
0.1
0.6
[1] 2q5q.a 0.2 0.3 0.1 0.4
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2nxw.a
2q5j.a
2q5l.a
2q5o.a
2q5q.a
[1] 2nxw.a
0
.05 .02 .04 .03
[1] 2q5j.a .05
0
.04 .09 .06
[1] 2q5l.a .02 .04
0
.06 .04
[1] 2q5o.a .04 .09 .06
0
.03
[1] 2q5q.a .03 .06 .04 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2nxw.a
2q5j.a
2q5l.a
2q5o.a
2q5q.a
[1] 2nxw.a
0
0.5 0.3 1.6 1.4
[1] 2q5j.a 0.5
0
0.4 1.7 1.4
[1] 2q5l.a 0.3 0.4
0
1.7 1.4
[1] 2q5o.a 1.6 1.7 1.7
0
0.3
[1] 2q5q.a 1.4 1.4 1.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
2nxw.a
2q5j.a
2q5l.a
2q5o.a
2q5q.a
[1] 2nxw.a
0
0.7 0.5 2.0 1.8
[1] 2q5j.a 0.7
0
0.6 2.1 1.9
[1] 2q5l.a 0.5 0.6
0
2.1 1.9
[1] 2q5o.a 2.0 2.1 2.1
0
0.5
[1] 2q5q.a 1.8 1.9 1.9 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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