Research workbench
Crystal structure of hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 6.0
Analyse Crystal structure of hansenula polymorpha copper amine oxidase-1 reduced by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KFD
- Type
- protein
- Length
- 3,933 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
- PEO, CU, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 656 | 15% helix, 39% strand | P12807 |
| C, D, E | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 655 | 15% helix, 39% strand | P12807 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 6 copies · chains A, B, C, D, E, F
- CU · Copper (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 3 copies · chains B, C, F
- GOL · Glycerol · additive · 52 copies · chains A, B, F, C, D, 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 | 698 | 0.89 | 0.93 | 116 | GOL |
| 2 | 484 | 0.86 | 0.93 | 85 | empty |
| 3 | 327 | 0.82 | 0.92 | 61 | GOL |
| 4 | 293 | 0.81 | 0.92 | 66 | GOL |
| 5 | 235 | 0.79 | 0.93 | 44 | empty |
Interfaces
12 interfaces between chains.
- E–F · 7276 Ų buried · 135 hydrogen bonds · protein-protein
- A–B · 7274 Ų buried · 135 hydrogen bonds · protein-protein
- C–D · 7261 Ų buried · 136 hydrogen bonds · protein-protein
- A–F · 542 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 537 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 6 modified (disulfide, nonstandard).
Compared structures
- 4KFD · Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine… · 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 E 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 4KFD · PDBe 4KFD · UniProt P12807
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