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BPHA1_RHOJR_1_460

Biphenyl 2,3-dioxygenase subunit alpha [Bacterial ring-hydroxylating dioxygenase alpha subunit family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BPHA1_RHOJR):R: Substrate binding (217, 218, 221, 222, 224, 225, 230)
274, 278, 311, 313, 323, 368, 374
217, 218, 221, 222, 224, 225, 230, 274, 278, 311, 313, 323, 368, 374
Metals (Me):Fe

Full PDB list

1uli, 1ulj

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
Q
2
1
7
F
2
1
8
D
2
2
1
M
2
2
2
H
2
2
4
A
2
2
5
H
2
3
0
L
2
7
4
I
2
7
8
A
3
1
1
H
3
1
3
L
3
2
3
F
3
6
8
F
3
7
4
[1]1uli.c none . . . . . . . . . . . . . . Fe
[1]1ulj.a bnl12 . . . . . . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 Me
Q
2
1
7
F
2
1
8
D
2
2
1
M
2
2
2
H
2
2
4
A
2
2
5
H
2
3
0
L
2
7
4
I
2
7
8
A
3
1
1
H
3
1
3
L
3
2
3
F
3
6
8
F
3
7
4
[1]1uli.c . . . . . . . . . . . . . . Fe
[1]1ulj.a . . . . . . . . . . . . . . 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
1uli.c is apo
1ulj.a:bnl
[1] 1uli.c
-
0.6
[1] 1ulj.a -
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
1uli.c
1ulj.a
[1] 1uli.c
0
.04
[1] 1ulj.a .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1uli.c
1ulj.a
[1] 1uli.c
0
0.5
[1] 1ulj.a 0.5
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
1uli.c
1ulj.a
[1] 1uli.c
0
0.6
[1] 1ulj.a 0.6
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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