Research workbench
Crystal structural of mutant Y305A in the copper amine oxidase from hansenula polymorpha
Analyse Crystal structural of mutant Y305A in the copper amine oxidase from hansenula… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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