Research workbench
Crystal structure of 6-hydoxy-D-nicotine oxidase from arthrobacter nicotinovorans. crystal form 2 (P21)
Analyse Crystal structure of 6-hydoxy-D-nicotine 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
- 2BVH
- Type
- protein
- Length
- 1,812 residues
- Chains
- 4
- 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
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 6-hydroxy-D-nicotine oxidase (EC 1.5.3.6) | protein | 453 | 31% helix, 24% strand | Q8GAG1 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.84 | 0.86 | 94 | FAD |
| 2 | 899 | 0.84 | 0.85 | 88 | FAD |
| 3 | 881 | 0.83 | 0.85 | 80 | FAD |
| 4 | 889 | 0.83 | 0.85 | 85 | FAD |
| 5 | 1144 | 0.81 | 0.82 | 111 | empty |
Interfaces
5 interfaces between chains.
- A–C · 728 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 550 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 505 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 247 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 219 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 2 disulfide (flavinylation, disulfide).
Compared structures
- 2BVH · 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 2BVH · PDBe 2BVH · UniProt Q8GAG1
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