Research workbench
Crystal structure of hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 8.5
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
- 4KFF
- Type
- protein
- Length
- 1,970 residues
- Chains
- 3
- 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 0.89
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 657 | 16% helix, 40% strand | P12807 |
| C | Peroxisomal primary amine oxidase (EC 1.4.3.21) | protein | 656 | 15% helix, 40% strand | P12807 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 14 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.89 | 0.91 | 153 | GOL |
| 2 | 1032 | 0.77 | 0.79 | 99 | GOL |
| 3 | 309 | 0.75 | 0.87 | 64 | empty |
| 4 | 244 | 0.71 | 0.86 | 41 | empty |
| 5 | 253 | 0.70 | 0.85 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–C · 7072 Ų buried · 140 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 243 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, nonstandard).
Compared structures
- 4KFF · Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine… · the same entry in another collection · chain A against A, 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 4KFF · PDBe 4KFF · UniProt P12807
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