MolNFT v1 · #32605 · protein
Crystal structure of 6-hydoxy-D-nicotine oxidase from arthrobacter nicotinovorans. crystal form 3 (P1)
2BVF · 6-hydroxy-D-nicotine oxidase: “Crystal structure of 6-hydoxy-D-nicotine oxidase from arthrobacter nicotinovorans. crystal form 3 (P1)”. X-ray diffraction, 1 ligand (FAD), 6 pockets (best druggability 0.82). MolNFT v1 #32605 on…
- PDB
- 2BVF
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-hydroxy-D-nicotine oxidase
- EC
- 1.5.3.6
- UniProt
- Q8GAG1
- Ligands
- FAD
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-hydroxy-D-nicotine oxidase (EC 1.5.3.6) | protein | 453 | 32% helix, 25% strand | Q8GAG1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 865 | 0.82 | 0.85 | 85 | FAD |
| 2 | 959 | 0.82 | 0.83 | 89 | FAD |
| 3 | 134 | 0.51 | 0.80 | 26 | empty |
| 4 | 114 | 0.50 | 0.81 | 30 | empty |
| 5 | 98 | 0.41 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 610 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 1 disulfide (flavinylation, disulfide).
Compared structures
- 2BVF · Crystal structure of 6-hydoxy-D-nicotine oxidase from Arthrobacter nicotinovorans.… · 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 Q8GAG1
- Elsewhere: RCSB PDB 2BVF · PDBe 2BVF · UniProt Q8GAG1
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