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AOX_TRYBB_1_329

Alternative oxidase, mitochondrial [Alternative oxidase family]

Composition of the binding site

Protein chains monomer
A1 (AOX_TRYBB):92, 95, 96, 99, 118, 119, 121:123, 125, 126, 162, 186, 190, 212, 213, 215, 216, 219, 220, 26692, 95, 96, 99, 118, 119, 121:123, 125, 126, 162, 186, 190, 212, 213, 215, 216, 219, 220, 266
Metals (Me):Fe

Full PDB list

3vv9, 3vva, 3w54, 5gn7, 5gn9

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
9
2
C
9
5
R
9
6
F
9
9
R
1
1
8
C
1
1
9
F
1
2
1
L
1
2
2
E
1
2
3
A
1
2
6
M
1
9
0
L
2
1
2
E
2
1
3
E
2
1
5
A
2
1
6
T
2
1
9
Y
2
2
0
E
2
6
6
[1]3vv9.b none . . . . . . . . . . . . . . . . . . Fe
[1]3vva.a chw24 . . . . . . . . . . . . . . . . . . Fe
[1]3w54.a rnb22 . . . . . . . . . . . . . . . . . . Fe
[1]5gn7.a 6xz28 . . . . . . . . . . . . . . . . . . Fe
[1]5gn9.a 6y017 . . . . . . . . . . . . . . . . . . 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
V
9
2
C
9
5
R
9
6
F
9
9
R
1
1
8
C
1
1
9
F
1
2
1
L
1
2
2
E
1
2
3
V
1
2
5
A
1
2
6
E
1
6
2
T
1
8
6
M
1
9
0
L
2
1
2
E
2
1
3
E
2
1
5
A
2
1
6
T
2
1
9
Y
2
2
0
E
2
6
6
[1]3vv9.b . . . . . . . . * . . . . . . . . . . . . Fe
[1]3vva.a . . . . . . . . . . . . . . . . . . . . . Fe
[1]3w54.a . . . . . . . . . . . . . . . . . . . . . Fe
[1]5gn7.a . . . . . . . . . . . . . . . . . . . . . Fe
[1]5gn9.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
3vv9.b is apo
3vva.a:chw
3w54.a:rnb
5gn7.a:6xz
5gn9.a:6y0
[1] 3vv9.b
-
0.7 0.9 1.4 1.3
[1] 3vva.a -
0
0 0.5 0.1
[1] 3w54.a - 0.1
0
0.7 0.1
[1] 5gn7.a - 0.2 0.2
0.5
0.5
[1] 5gn9.a - 0.3 0.3 0.9
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
3vv9.b
3vva.a
3w54.a
5gn7.a
5gn9.a
[1] 3vv9.b
0
.10 .10 .08 .10
[1] 3vva.a .10
0
.02 .05 .04
[1] 3w54.a .10 .02
0
.05 .03
[1] 5gn7.a .08 .05 .05
0
.06
[1] 5gn9.a .10 .04 .03 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
3vv9.b
3vva.a
3w54.a
5gn7.a
5gn9.a
[1] 3vv9.b
0
0.5 0.4 0.4 0.4
[1] 3vva.a 0.5
0
0.3 0.5 0.5
[1] 3w54.a 0.4 0.3
0
0.4 0.4
[1] 5gn7.a 0.4 0.5 0.4
0
0.4
[1] 5gn9.a 0.4 0.5 0.4 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
3vv9.b
3vva.a
3w54.a
5gn7.a
5gn9.a
[1] 3vv9.b
0
0.7 0.6 0.6 0.7
[1] 3vva.a 0.7
0
0.4 0.6 0.6
[1] 3w54.a 0.6 0.4
0
0.6 0.6
[1] 5gn7.a 0.6 0.6 0.6
0
0.5
[1] 5gn9.a 0.7 0.6 0.6 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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