Research workbench
Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, BSU39980) from bacillus subtilis at 2.60 a resolution
Analyse Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, BSU39980) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H0V
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quercetin 2,3-dioxygenase
- EC
- 1.13.11.24
- UniProt
- P42106
- Ligands
- FE
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Quercetin 2,3-dioxygenase (EC 1.13.11.24) | protein | 335 | 10% helix, 40% strand | P42106 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.85 | 0.87 | 102 | EDO |
| 2 | 220 | 0.76 | 0.90 | 42 | TLA |
| 3 | 246 | 0.75 | 0.88 | 38 | TLA |
| 4 | 124 | 0.43 | 0.76 | 32 | EDO |
| 5 | 121 | 0.42 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1467 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2H0V · Crystal structure of a putative quercetin 2,3-dioxygenase (yxag, bsu39980) from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P42106 · AlphaFold monomer V2.0 prediction for quercetin 2,3-dioxygenase (P42106) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P42106
- Elsewhere: RCSB PDB 2H0V · PDBe 2H0V · UniProt P42106
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.