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C562_ECOLX_23_128_quin

Soluble cytochrome b562 [Cytochrome b562 family]

Composition of the binding site

Protein chains monomer
A1 (C562_ECOLX):85, 88, 89, 92, 9385, 88, 89, 92, 93
Metals (Me):Fe

Full PDB list

1lm3, 1m6t, 256b, 2bc5, 2qla, 3c62, 3c63, 3de8, 3de9, 3foo, 3fop, 3l1m, 3nmi, 3nmj, 3nmk, 5awi (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
H
8
5
D
8
8
I
8
9
G
9
2
Q
9
3
[1]256b.a none . . . . . Fe
[1]2qla.a zn1 . . . . . Fe
[1]3c62.a none . . . . . Fe
[1]3l1m.a hqi,ni16 . . . C . Fe
[1]3nmi.a none A A . . . Fe
[2]3foo.a none A H . . . 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
H
8
5
D
8
8
I
8
9
G
9
2
Q
9
3
[1]256b.a . . . . . Fe
[1]2qla.a . . . . . Fe
[1]3c62.a * . . . . Fe
[1]3l1m.a . . . C . Fe
[1]3nmi.a A A . . . Fe
[2]3foo.a A H . . . 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
256b.a is apo
2qla.a:zn
3c62.a is apo
3l1m.a:hqi,ni
3nmi.a is apo
3foo.a is apo
[1] 256b.a
-
0.2 - 0.1 - -
[1] 2qla.a -
0.1
- 0.1 - -
[1] 3c62.a - 0.6
-
0.4 - -
[1] 3l1m.a - 0.2 -
0.7
- -
[1] 3nmi.a - 0 - 0
-
-
[2] 3foo.a - 0 - 1.3 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
256b.a
2qla.a
3c62.a
3l1m.a
3nmi.a
3foo.a
[1] 256b.a
0
.03 .07 .10 .03 .25
[1] 2qla.a .03
0
.10 .13 .03 .22
[1] 3c62.a .07 .10
0
.17 .10 .32
[1] 3l1m.a .10 .13 .17
0
.13 .35
[1] 3nmi.a .03 .03 .10 .13
0
.22
[2] 3foo.a .25 .22 .32 .35 .22
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

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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
256b.a
2qla.a
3c62.a
3l1m.a
3nmi.a
3foo.a
[1] 256b.a
0
0.3 0.3 0.2 0.4 0.2
[1] 2qla.a 0.3
0
0.3 0.3 0.3 0.3
[1] 3c62.a 0.3 0.3
0
0.4 0.3 0.3
[1] 3l1m.a 0.2 0.3 0.4
0
0.4 0.2
[1] 3nmi.a 0.4 0.3 0.3 0.4
0
0.3
[2] 3foo.a 0.2 0.3 0.3 0.2 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

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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
256b.a
2qla.a
3c62.a
3l1m.a
3nmi.a
3foo.a
[1] 256b.a
0
1.0 0.8 0.6 0.4 0.8
[1] 2qla.a 1.0
0
0.8 0.9 1.0 0.8
[1] 3c62.a 0.8 0.8
0
0.9 0.6 0.7
[1] 3l1m.a 0.6 0.9 0.9
0
0.7 0.6
[1] 3nmi.a 0.4 1.0 0.6 0.7
0
0.7
[2] 3foo.a 0.8 0.8 0.7 0.6 0.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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