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AOC3_HUMAN_30_763

Membrane primary amine oxidase [Copper/topaquinone oxidase family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (AOC3_HUMAN):R: Substrate binding (389, 394)
R: Substrate binding (468, 469, 471)
173, 176, 177, 180, 210:212, 227, 762
173, 176, 177, 180, 210:212, 227, 389, 394, 468, 469, 471, 762
A2 (AOC3_HUMAN):447, 448447, 448
Metals (Me):Cu

Full PDB list

1pu4, 1us1, 2c10, 2c11, 2y73, 2y74, 4btw, 4btx, 4bty (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
F
1
7
3
Y
1
7
6
L
1
7
7
D
1
8
0
T
2
1
0
T
2
1
2
F
2
2
7
F
3
8
9
Y
3
9
4
L
4
6
8
L
4
6
9
H
7
6
2
L
4
4
7
Y
4
4
8
[1]2c11.a none . . . . . . . . . . . - . . Cu
[1]2y73.a none . . . . . . . . . . . . . . Cu
[1]2y74.b none . . . . . . . . . . . - . .
[1]4btw.a jw725 . . . . . . . . . . . . . . Cu
[1]4btx.a wf822 . . . . . . . . . . . . . . Cu
[1]4bty.a jwf33 . . . . . . . . . . . . . . Cu

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 A2 Me
F
1
7
3
Y
1
7
6
L
1
7
7
D
1
8
0
T
2
1
0
M
2
1
1
T
2
1
2
F
2
2
7
F
3
8
9
Y
3
9
4
L
4
6
8
L
4
6
9
Y
4
7
1
H
7
6
2
L
4
4
7
Y
4
4
8
[1]2c11.a . . . . . . . . . . . . * - . . Cu
[1]2y73.a * . . . . . . . . . . . * . . . Cu
[1]2y74.b * . . . . . . . . . . . * - . .
[1]4btw.a . . . . . . . . . . . . * * . . Cu
[1]4btx.a . . . . . . . . . . . . * . . . Cu
[1]4bty.a . . . . . . . . . . . . * . . . Cu

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
2c11.a is apo
2y73.a is apo
2y74.b is apo
4btw.a:jw7
4btx.a:wf8
4bty.a:jwf
[1] 2c11.a
-
- - 1.4 1.1 1.8
[1] 2y73.a -
-
- 2.4 1.9 3.2
[1] 2y74.b - -
-
2.6 1.5 3.0
[1] 4btw.a - - -
0.1
0.1 1.7
[1] 4btx.a - - - 0.4
0
0.5
[1] 4bty.a - - - 0.4 0.2
0.2
[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
2c11.a
2y73.a
2y74.b
4btw.a
4btx.a
4bty.a
[1] 2c11.a
0
.21 .19 .22 .11 .13
[1] 2y73.a .21
0
.02 .28 .18 .19
[1] 2y74.b .19 .02
0
.29 .19 .20
[1] 4btw.a .22 .28 .29
0
.11 .12
[1] 4btx.a .11 .18 .19 .11
0
.03
[1] 4bty.a .13 .19 .20 .12 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.5 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
2c11.a
2y73.a
2y74.b
4btw.a
4btx.a
4bty.a
[1] 2c11.a
0
0.3 0.3 0.5 0.4 0.4
[1] 2y73.a 0.3
0
0.2 0.7 0.4 1.3
[1] 2y74.b 0.3 0.2
0
0.4 0.3 0.3
[1] 4btw.a 0.5 0.7 0.4
0
0.6 1.4
[1] 4btx.a 0.4 0.4 0.3 0.6
0
1.4
[1] 4bty.a 0.4 1.3 0.3 1.4 1.4
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
2c11.a
2y73.a
2y74.b
4btw.a
4btx.a
4bty.a
[1] 2c11.a
0
2.0 1.6 1.5 1.4 1.5
[1] 2y73.a 2.0
0
1.0 2.1 1.6 2.2
[1] 2y74.b 1.6 1.0
0
1.2 1.1 1.2
[1] 4btw.a 1.5 2.1 1.2
0
1.5 1.1
[1] 4btx.a 1.4 1.6 1.1 1.5
0
1.8
[1] 4bty.a 1.5 2.2 1.2 1.1 1.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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