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Crystal structure of Y305F mutant of the copper amine oxidase from hansenula polymorpha expressed in yeast
Analyse Crystal structure of Y305F mutant of 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
- 3NBJ
- 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, PO4
- Pockets
- 20 · best druggability 0.89
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 | 655 | 15% 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 · 18 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 | 965 | 0.89 | 0.91 | 130 | empty |
| 2 | 563 | 0.88 | 0.93 | 82 | empty |
| 3 | 536 | 0.87 | 0.93 | 89 | empty |
| 4 | 344 | 0.83 | 0.93 | 66 | empty |
| 5 | 296 | 0.82 | 0.93 | 49 | empty |
Interfaces
12 interfaces between chains.
- C–D · 7142 Ų buried · 129 hydrogen bonds · protein-protein
- A–B · 7139 Ų buried · 128 hydrogen bonds · protein-protein
- E–F · 7138 Ų buried · 130 hydrogen bonds · protein-protein
- A–F · 540 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 6 disulfide (nonstandard, disulfide).
Compared structures
- 3NBJ · Crystal Structure of Y305F mutant of 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 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 3NBJ · PDBe 3NBJ · UniProt P12807
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