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Structure of 2,6-dihydroxypyridine-3-hydroxylase from Arthrobacter nicotinovorans
Analyse Structure of 2,6-dihydroxypyridine-3-hydroxylase from Arthrobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VOU
- Type
- protein
- Length
- 1,167 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- ARTHROBACTER NICOTINOVORANS
- Molecule
- 2,6-dihydroxypyridine hydroxylase
- EC
- 1.14.13.10
- UniProt
- Q93NG3
- Ligands
- FAD
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,6-dihydroxypyridine hydroxylase (EC 1.14.13.10) | protein | 393 | 35% helix, 26% strand | Q93NG3 |
| B, C | 2,6-dihydroxypyridine hydroxylase (EC 1.14.13.10) | protein | 387 | 36% helix, 27% strand | Q93NG3 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.82 | 0.84 | 87 | FAD, GOL, ACT |
| 2 | 893 | 0.82 | 0.84 | 82 | FAD, GOL, ACT |
| 3 | 978 | 0.79 | 0.81 | 78 | FAD, GOL, ACT |
| 4 | 156 | 0.55 | 0.81 | 21 | empty |
| 5 | 174 | 0.50 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- B–C · 959 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 398 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 239 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VOU · Structure of 2,6-dihydroxypyridine-3-hydroxylase from arthrobacter nicotinovorans · the same entry in another collection · chain A against A, TM-score 1.00
- Q93NG3 · AlphaFold monomer V2.0 prediction for 2,6-dihydroxypyridine 3-monooxygenase (Q93NG3) · 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 Q93NG3
- Elsewhere: RCSB PDB 2VOU · PDBe 2VOU · UniProt Q93NG3
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