MolNFT v1 · #55858 · protein
Crystal structure of D298K copper amine oxidase from arthrobacter globiformis
2YX9 · Phenylethylamine oxidase: “Crystal structure of D298K copper amine oxidase from arthrobacter globiformis”. X-ray diffraction, 1 ligand (CU), 17 pockets (best druggability 0.90). MolNFT v1 #55858 on GenesisL1: 3D structure, binding…
- PDB
- 2YX9
- Type
- protein
- Length
- 1,240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylethylamine oxidase
- EC
- 1.4.3.6
- UniProt
- P46881
- Ligands
- CU
- Pockets
- 17 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylethylamine oxidase (EC 1.4.3.6) | protein | 620 | 13% helix, 43% strand | P46881 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.90 | 0.91 | 138 | empty |
| 2 | 364 | 0.74 | 0.85 | 53 | empty |
| 3 | 358 | 0.70 | 0.83 | 64 | empty |
| 4 | 295 | 0.65 | 0.81 | 36 | empty |
| 5 | 327 | 0.64 | 0.80 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 6794 Ų buried · 103 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 2YX9 · Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis · the same entry in another collection · chain A 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 P46881
- Elsewhere: RCSB PDB 2YX9 · PDBe 2YX9 · UniProt P46881
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