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Crystal structure at 2.5 a resolution of zinc-substituted copper amine oxidase of hansenula polymorpha expressed in escherichia COLI
Analyse Crystal structure at 2.5 a resolution of zinc-substituted copper amine oxidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EKM
- Type
- protein
- Length
- 1,968 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- P12807
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Copper amine oxidase (EC 1.4.3.6) | protein | 656 | 16% helix, 40% strand | P12807 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.89 | 0.91 | 145 | empty |
| 2 | 400 | 0.73 | 0.83 | 76 | empty |
| 3 | 225 | 0.72 | 0.88 | 36 | empty |
| 4 | 229 | 0.72 | 0.87 | 39 | empty |
| 5 | 190 | 0.72 | 0.89 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 7266 Ų buried · 142 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1EKM · Crystal structure at 2.5 a resolution of zinc-substituted copper amine oxidase of… · 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 1EKM · PDBe 1EKM · UniProt P12807
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