Research workbench
Crystal structure of nickel-substituted amine oxidase from arthrobacter globiformis
Analyse Crystal structure of nickel-substituted amine oxidase from arthrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IQY
- Type
- protein
- Length
- 1,240 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase
- EC
- 1.4.3.6
- UniProt
- P46881
- Ligands
- NI
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amine oxidase (EC 1.4.3.6) | protein | 620 | 11% helix, 42% strand | P46881 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.90 | 0.91 | 144 | empty |
| 2 | 315 | 0.72 | 0.85 | 56 | empty |
| 3 | 64 | 0.69 | 0.96 | 27 | empty |
| 4 | 240 | 0.65 | 0.83 | 34 | empty |
| 5 | 267 | 0.63 | 0.81 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 6751 Ų buried · 104 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 1IQY · Crystal structure of nickel-substituted amine oxidase from arthrobacter globiformis · the same entry in another collection · chain A against A, TM-score 1.00
- P46881 · AlphaFold monomer V2.0 prediction for phenylethylamine oxidase (P46881) · a predicted model of the same protein · 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 1IQY · PDBe 1IQY · UniProt P46881
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