Research workbench
The active site base controls cofactor reactivity in escherichia COLI amine oxidase : X-ray crystallographic studies with mutational variants
Analyse The active site base controls cofactor reactivity in escherichia COLI amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QAL
- Type
- protein
- Length
- 1,439 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper amine oxidase
- EC
- 1.4.3.4
- UniProt
- P46883
- Ligands
- CA, CU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper amine oxidase (EC 1.4.3.4) | protein | 718 | 13% helix, 44% strand | P46883 |
| B | Copper amine oxidase (EC 1.4.3.4) | protein | 721 | 12% helix, 44% strand | P46883 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B
- 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
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 866 | 0.87 | 0.89 | 99 | empty |
| 2 | 304 | 0.77 | 0.88 | 52 | empty |
| 3 | 256 | 0.71 | 0.86 | 44 | empty |
| 4 | 334 | 0.69 | 0.82 | 37 | empty |
| 5 | 338 | 0.65 | 0.80 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 7169 Ų buried · 142 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1QAL · The active site base controls cofactor reactivity in escherichia COLI amine oxidase… · the same entry in another collection · chain A against A, TM-score 1.00
- P46883 · AlphaFold monomer V2.0 prediction for primary amine oxidase (P46883) · 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 P46883
- Elsewhere: RCSB PDB 1QAL · PDBe 1QAL · UniProt P46883
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