MolNFT v1 · #14026 · protein
Crystal structure of E. COLI amine oxidase complexed with tranylcypromine
1LVN · Copper amine oxidase: “Crystal structure of E. COLI amine oxidase complexed with tranylcypromine”. X-ray diffraction, 3 ligands (TYT, CA, CU), 20 pockets (best druggability 0.87). MolNFT v1 #14026 on GenesisL1: 3D structure, binding…
- PDB
- 1LVN
- Type
- protein
- Length
- 1,436 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
- TYT, CA, CU
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Copper amine oxidase (EC 1.4.3.6) | protein | 717 | 12% helix, 44% strand | P46883 |
| B | Copper amine oxidase (EC 1.4.3.6) | protein | 719 | 13% helix, 44% strand | P46883 |
Ligands and binding sites
- TYT · Tyrosine derivative · ligand · 2 copies · chains A, B
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.87 | 0.91 | 71 | empty |
| 2 | 767 | 0.83 | 0.86 | 116 | TYT |
| 3 | 908 | 0.75 | 0.78 | 98 | empty |
| 4 | 398 | 0.75 | 0.85 | 59 | TYT |
| 5 | 256 | 0.69 | 0.85 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 7279 Ų buried · 139 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1LVN · Crystal structure of E. COLI amine oxidase complexed with tranylcypromine · 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 1LVN · PDBe 1LVN · UniProt P46883
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