Research workbench
Crystal structure of quercetin 2,3-dioxygenase
Analyse Crystal structure of quercetin 2,3-dioxygenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JUH
- Type
- protein
- Length
- 1,337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quercetin 2,3-dioxygenase
- EC
- 1.13.11.24
- UniProt
- Q7SIC2
- Ligands
- NAG, MAN, BMA, CU
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quercetin 2,3-dioxygenase (EC 1.13.11.24) | protein | 334 | 9% helix, 39% strand | Q7SIC2 |
| B | Quercetin 2,3-dioxygenase (EC 1.13.11.24) | protein | 339 | 9% helix, 38% strand | Q7SIC2 |
| C | Quercetin 2,3-dioxygenase (EC 1.13.11.24) | protein | 334 | 9% helix, 39% strand | Q7SIC2 |
| D | Quercetin 2,3-dioxygenase (EC 1.13.11.24) | protein | 330 | 9% helix, 39% strand | Q7SIC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, C, B, D
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains C, A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, A
- CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 32 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.80 | 0.95 | 37 | EDO |
| 2 | 822 | 0.71 | 0.77 | 80 | NAG, EDO |
| 3 | 52 | 0.70 | 0.98 | 22 | empty |
| 4 | 435 | 0.69 | 0.81 | 53 | empty |
| 5 | 147 | 0.67 | 0.87 | 29 | empty |
Interfaces
2 interfaces between chains.
- A–C · 2198 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 577 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan (N-glycosylation).
Compared structures
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 Q7SIC2
- Elsewhere: RCSB PDB 1JUH · PDBe 1JUH · UniProt Q7SIC2
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