Research workbench
Crystal structure of mutant Y305F expressed in E. COLI in the copper amine oxidase from hansenula polymorpha
Analyse Crystal structure of mutant Y305F expressed in E. COLI in the copper amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NBB
- Type
- protein
- Length
- 3,966 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 · 15% 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 | 661 | 15% 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 | 989 | 0.90 | 0.93 | 168 | empty |
| 2 | 365 | 0.83 | 0.92 | 72 | empty |
| 3 | 260 | 0.80 | 0.92 | 56 | empty |
| 4 | 226 | 0.79 | 0.93 | 42 | empty |
| 5 | 209 | 0.79 | 0.93 | 36 | empty |
Interfaces
12 interfaces between chains.
- C–D · 7084 Ų buried · 145 hydrogen bonds · protein-protein
- E–F · 7080 Ų buried · 146 hydrogen bonds · protein-protein
- A–B · 7079 Ų buried · 144 hydrogen bonds · protein-protein
- B–C · 531 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 514 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 6 disulfide (nonstandard, disulfide).
Compared structures
- 3NBB · Crystal structure of mutant Y305F expressed in E. coli in the copper amine oxidase from… · 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 0.99
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 3NBB · PDBe 3NBB · UniProt P12807
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