MolNFT v1 · #3911 · protein
Crystal structure of the aerobically freeze trapped rate-determining catalytic intermediate of E. COLI copper-containing amine oxidase.
1D6Z · Copper amine oxidase: “Crystal structure of the aerobically freeze trapped rate-determining catalytic intermediate of E. COLI…”. X-ray diffraction, 5 ligands (HY1, PEO, PEA), 20 pockets (best druggability 0.86). MolNFT v1 #3911 on…
- PDB
- 1D6Z
- Type
- protein
- Length
- 1,438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Copper amine oxidase
- EC
- 1.4.3.6
- UniProt
- P46883
- Ligands
- HY1, PEO, PEA, CA, CU
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper amine oxidase (EC 1.4.3.6) | protein | 718 | 13% helix, 45% strand | P46883 |
| B | Copper amine oxidase (EC 1.4.3.6) | protein | 720 | 12% helix, 44% strand | P46883 |
Ligands and binding sites
- HY1 · Phenylacetaldehyde · ligand · 2 copies · chains A, B
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B
- PEA · 2-phenylethylamine · ligand · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.86 | 0.90 | 70 | GOL |
| 2 | 385 | 0.76 | 0.86 | 65 | empty |
| 3 | 324 | 0.73 | 0.85 | 60 | empty |
| 4 | 355 | 0.68 | 0.81 | 60 | HY1 |
| 5 | 315 | 0.65 | 0.81 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 7232 Ų buried · 144 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1D6Z · Crystal structure of the aerobically freeze trapped rate-determining catalytic… · 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 1D6Z · PDBe 1D6Z · UniProt P46883
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