MolNFT v1 · #72466 · protein
Crystal structural of mutant Y305A in the copper amine oxidase from hansenula polymorpha
3N9H · Peroxisomal primary amine oxidase: “Crystal structural of mutant Y305A in the copper amine oxidase from hansenula polymorpha”. X-ray diffraction, 1 ligand (CU), 20 pockets (best druggability 0.90). MolNFT v1 #72466 on GenesisL1: 3D…
- PDB
- 3N9H
- Type
- protein
- Length
- 3,930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisomal primary amine oxidase
- EC
- 1.4.3.21
- UniProt
- P12807
- Ligands
- CU
- Pockets
- 20 · best druggability 0.90
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 | Peroxisomal primary amine oxidase (EC 1.4.3.21) | 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
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 | 997 | 0.90 | 0.91 | 135 | empty |
| 2 | 399 | 0.85 | 0.93 | 72 | empty |
| 3 | 393 | 0.84 | 0.92 | 69 | empty |
| 4 | 261 | 0.81 | 0.93 | 46 | empty |
| 5 | 216 | 0.80 | 0.94 | 41 | empty |
Interfaces
12 interfaces between chains.
- E–F · 7223 Ų buried · 132 hydrogen bonds · protein-protein
- C–D · 7221 Ų buried · 130 hydrogen bonds · protein-protein
- A–B · 7215 Ų buried · 131 hydrogen bonds · protein-protein
- B–C · 518 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 517 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (nonstandard).
Compared structures
- 3N9H · Crystal Structural of mutant Y305A in the copper amine oxidase from hansenula polymorpha · 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 B 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 3N9H · PDBe 3N9H · UniProt P12807
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