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Crystal structure of copper amine oxidase from arthrobacter globiformis in the presence of sodium bromide
Analyse Crystal structure of copper amine oxidase from arthrobacter globiformis in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X42
- Type
- protein
- Length
- 1,242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylethylamine oxidase
- EC
- 1.4.3.21
- UniProt
- P46881
- Ligands
- CU, NA, K, BR
- Pockets
- 17 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phenylethylamine oxidase (EC 1.4.3.21) | protein | 621 | 13% helix, 43% strand | P46881 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 13 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.89 | 0.91 | 132 | BR, GOL |
| 2 | 345 | 0.73 | 0.85 | 57 | empty |
| 3 | 363 | 0.70 | 0.83 | 57 | GOL |
| 4 | 324 | 0.66 | 0.81 | 39 | empty |
| 5 | 290 | 0.64 | 0.81 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 6854 Ų buried · 106 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 3X42 · Crystal structure of copper amine oxidase from Arthrobacter globiformis in the presence… · 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 3X42 · PDBe 3X42 · UniProt P46881
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