MolNFT v1 · #47112 · protein
Crystal structure of hansenula polymorpha amine oxidase to 1.7 ångströms
2OOV · Peroxisomal copper amine oxidase: “Crystal structure of hansenula polymorpha amine oxidase to 1.7 ångströms”. X-ray diffraction, 2 ligands (CU, PO4), 20 pockets (best druggability 0.89). MolNFT v1 #47112 on GenesisL1: 3D structure…
- PDB
- 2OOV
- Type
- protein
- Length
- 3,930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- P12807
- Ligands
- CU, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisomal copper amine oxidase (EC 1.4.3.6) | protein | 655 | 15% helix, 40% strand | P12807 |
| C, D, E, F | Peroxisomal copper amine 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, D, E, F
- PO4 · Phosphate ion · ion · 2 copies · chains C, F
- GOL · Glycerol · additive · 28 copies · chains A, B, F, D, C, E
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.89 | 0.91 | 161 | GOL |
| 2 | 690 | 0.89 | 0.93 | 123 | GOL |
| 3 | 252 | 0.80 | 0.92 | 49 | empty |
| 4 | 206 | 0.78 | 0.93 | 43 | empty |
| 5 | 211 | 0.78 | 0.92 | 39 | empty |
Interfaces
12 interfaces between chains.
- A–B · 7296 Ų buried · 140 hydrogen bonds · protein-protein
- E–F · 7201 Ų buried · 138 hydrogen bonds · protein-protein
- C–D · 7115 Ų buried · 136 hydrogen bonds · protein-protein
- A–F · 573 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 559 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified, 6 disulfide (nonstandard, disulfide).
Compared structures
- 2OOV · Crystal Structure of Hansenula polymorpha amine oxidase to 1.7 Angstroms · the same entry in another collection · chain F against F, TM-score 1.00
- P12807 · AlphaFold monomer V2.0 prediction for peroxisomal primary amine oxidase (P12807) · a predicted model of the same protein · chain F 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 2OOV · PDBe 2OOV · UniProt P12807
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