MolNFT v1 · #315 · protein

Copper amine oxidase from hansenula polymorpha

1A2V · Methylamine oxidase: “Copper amine oxidase from hansenula polymorpha”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.88). MolNFT v1 #315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1A2V
Type: protein
Length: 3,930 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methylamine oxidase
EC: 1.4.3.6
UniProt: P12807
Ligands: CU
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 16% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Methylamine oxidase (EC 1.4.3.6)	protein	655	16% helix, 40% strand	P12807

Ligands and binding sites

CU · Copper (II) ion · metal · 6 copies · chains A, B, C, F, E, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	847	0.88	0.91	112	empty
2	431	0.85	0.92	83	empty
3	283	0.82	0.93	46	empty
4	290	0.82	0.93	58	empty
5	275	0.81	0.93	45	empty

Interfaces

12 interfaces between chains.

C–D · 7177 Å² buried · 129 hydrogen bonds · protein-protein
A–B · 7170 Å² buried · 131 hydrogen bonds · protein-protein
E–F · 7159 Å² buried · 132 hydrogen bonds · protein-protein
A–F · 535 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 533 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified, 1 disulfide (nonstandard, disulfide).

Compared structures

1A2V · Copper amine oxidase from hansenula polymorpha · the same entry in another collection · chain C against C, TM-score 1.00
P12807 · AlphaFold monomer V2.0 prediction for peroxisomal primary amine oxidase (P12807) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P12807
Elsewhere: RCSB PDB 1A2V · PDBe 1A2V · UniProt P12807

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