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DCIP_AZOBR_2_545_allosteric

Indole-3-pyruvate decarboxylase [TPP enzyme family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DCIP_AZOBR):R: Thiamine pyrophosphate binding (394:397)
60, 61, 214, 215, 237, 238, 240:242, 375
60, 61, 214, 215, 237, 238, 240:242, 375, 394:397

Full PDB list

2nxw, 2q5j, 2q5l, 2q5o, 2q5q (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
6
0
Y
6
1
R
2
1
4
R
2
1
5
M
2
3
8
R
2
4
0
G
2
4
1
L
2
4
2
L
3
7
5
G
3
9
4
L
3
9
5
M
3
9
6
A
3
9
7
[1]2nxw.a none . . . . . . . . . . . . .
[1]2q5o.a ppy12 . . . . . . . . . . . . .
[1]2q5q.a kpv14 . . . . . . . . . . . . .

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
R
6
0
Y
6
1
R
2
1
4
R
2
1
5
F
2
3
7
M
2
3
8
R
2
4
0
G
2
4
1
L
2
4
2
L
3
7
5
G
3
9
4
L
3
9
5
M
3
9
6
A
3
9
7
[1]2nxw.a . . . . . . . . . . . . . .
[1]2q5o.a . . . . . . . . . . . . . .
[1]2q5q.a . . . . . . . . . . . . . .

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 is apo
2q5o.a:ppy
2q5q.a:kpv
[1] 2nxw.a
-
0.2 0
[1] 2q5o.a -
0
0.6
[1] 2q5q.a - 0
0
[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
2q5o.a
2q5q.a
[1] 2nxw.a
0
.04 .01
[1] 2q5o.a .04
0
.04
[1] 2q5q.a .01 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 Å)

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

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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
2q5o.a
2q5q.a
[1] 2nxw.a
0
2.4 2.4
[1] 2q5o.a 2.4
0
0.3
[1] 2q5q.a 2.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2q5o.a
2q5q.a
[1] 2nxw.a
0
2.5 2.5
[1] 2q5o.a 2.5
0
0.4
[1] 2q5q.a 2.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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