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BPHC_PSES1_2_293

Biphenyl-2,3-diol 1,2-dioxygenase [Extradiol ring-cleavage dioxygenase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BPHC_PSES1):D: VOC 2 (146, 148, 173, 175, 187, 195, 202, 209, 210, 241, 243, 244, 250, 261)
281
146, 148, 173, 175, 187, 195, 202, 209, 210, 241, 243, 244, 250, 261, 281
Metals (Me):Fe

Full PDB list

1dhy, 1eil, 1eiq, 1eir, 1kw3, 1kw6, 1kw8, 1kw9, 1kwb, 1kwc (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
1
4
6
V
1
4
8
I
1
7
3
I
1
7
5
F
1
8
7
H
1
9
5
F
2
0
2
H
2
0
9
H
2
1
0
H
2
4
1
N
2
4
3
D
2
4
4
Y
2
5
0
E
2
6
1
T
2
8
1
[1]1dhy.a none . . . . . . . . . . . . . . . Fe
[1]1eir.a bpy14 . . . . . . . . . . . . . . . Fe
[1]1kwb.b none A . . . . . . . . . . . . . .
[1]1kwc.b bpy14 A . . . . . . . . . . . . . .

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 Me
H
1
4
6
V
1
4
8
I
1
7
3
I
1
7
5
F
1
8
7
H
1
9
5
F
2
0
2
H
2
0
9
H
2
1
0
H
2
4
1
N
2
4
3
D
2
4
4
Y
2
5
0
E
2
6
1
T
2
8
1
[1]1dhy.a . . . . . . . . . . . . . . . Fe
[1]1eir.a . . . . . . . . . . . . . . . Fe
[1]1kwb.b A . . . . . . . . . . . . . .
[1]1kwc.b 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
1dhy.a is apo
1eir.a:bpy
1kwb.b is apo
1kwc.b:bpy
[1] 1dhy.a
-
0.1 - 0.2
[1] 1eir.a -
0
- 0
[1] 1kwb.b - 0
-
0.1
[1] 1kwc.b - 0 -
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
1dhy.a
1eir.a
1kwb.b
1kwc.b
[1] 1dhy.a
0
.01 .01 .02
[1] 1eir.a .01
0
.01 .01
[1] 1kwb.b .01 .01
0
.01
[1] 1kwc.b .02 .01 .01
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
1dhy.a
1eir.a
1kwb.b
1kwc.b
[1] 1dhy.a
0
0.2 0.3 0.2
[1] 1eir.a 0.2
0
0.2 0.2
[1] 1kwb.b 0.3 0.2
0
0.2
[1] 1kwc.b 0.2 0.2 0.2
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

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
1dhy.a
1eir.a
1kwb.b
1kwc.b
[1] 1dhy.a
0
0.8 0.8 0.8
[1] 1eir.a 0.8
0
0.4 0.5
[1] 1kwb.b 0.8 0.4
0
0.4
[1] 1kwc.b 0.8 0.5 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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