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AMNB_COMTE_1_312

2-aminophenol 1,6-dioxygenase subunit beta [LigB/MhpB extradiol dioxygenase family]

Composition of the binding site

Protein chains monomer
A1 (AMNB_COMTE):13:16, 62, 86, 129, 192, 195, 251, 279, 280, 28213:16, 62, 86, 129, 192, 195, 251, 279, 280, 282
Metals (Me):Fe

Full PDB list

3vsg, 3vsh, 3vsi, 3vsj (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
H
1
3
P
1
4
P
1
5
H
1
6
H
6
2
F
8
6
Y
1
2
9
T
1
9
2
H
1
9
5
E
2
5
1
V
2
7
9
I
2
8
0
T
2
8
2
[1]3vsh.b none . . . . . . . . . . . . . Fe
[1]3vsi.b 4nc11 . . . . . . . . . . . . . Fe
[1]3vsj.b 2xp10 . . . . . . . . . . . . . Fe

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

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PDB.ch
A1 Me
H
1
3
P
1
4
P
1
5
H
1
6
H
6
2
F
8
6
Y
1
2
9
T
1
9
2
H
1
9
5
E
2
5
1
V
2
7
9
I
2
8
0
T
2
8
2
[1]3vsh.b . . . . . . . . . . . . . Fe
[1]3vsi.b . . . . . . . . . . . . . Fe
[1]3vsj.b . . . . . . . . . . . . . Fe

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
3vsh.b is apo
3vsi.b:4nc
3vsj.b:2xp
[1] 3vsh.b
-
0.6 0.2
[1] 3vsi.b -
0.1
0.1
[1] 3vsj.b - 0.1
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
3vsh.b
3vsi.b
3vsj.b
[1] 3vsh.b
0
.05 .04
[1] 3vsi.b .05
0
.02
[1] 3vsj.b .04 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
3vsh.b
3vsi.b
3vsj.b
[1] 3vsh.b
0
0.4 0.2
[1] 3vsi.b 0.4
0
0.4
[1] 3vsj.b 0.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
3vsh.b
3vsi.b
3vsj.b
[1] 3vsh.b
0
0.9 0.6
[1] 3vsi.b 0.9
0
1.0
[1] 3vsj.b 0.6 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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