Research workbench
Oxidized structure of bovine xanthine oxidoreductase bound with oxypurinol.
Analyse Oxidized structure of bovine xanthine oxidoreductase bound with oxypurinol. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D6O
- Type
- protein
- Length
- 2,573 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine DEHYDROGENASE/OXIDASE
- EC
- 1.17.1.4, 1.17.3.2
- UniProt
- P80457
- Ligands
- FES, MTE, MOS, FAD, 141, CA, CO3
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1285 | 34% helix, 23% strand | P80457 |
| B | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1288 | 33% helix, 23% strand | P80457 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
- MTE · Phosphonic acidmono-(2-amino-5,6-dimercapto-4-oxo-3,7,8A,9,10,10A-hexahydro-4H-8-oxa-1,3,9,10-tetraaza-anthracen-7-ylmethyl)ester · ligand · 2 copies · chains A, B
- MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 141 · Oxypurinol · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CO3 · Carbonate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 732 | 0.84 | 0.87 | 72 | empty |
| 2 | 901 | 0.84 | 0.85 | 121 | empty |
| 3 | 1005 | 0.84 | 0.84 | 109 | empty |
| 4 | 736 | 0.83 | 0.87 | 75 | empty |
| 5 | 761 | 0.83 | 0.86 | 87 | FAD |
Interfaces
1 interface between chains.
- A–B · 3149 Ų buried · 59 hydrogen bonds · protein-protein
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 P80457
- Elsewhere: RCSB PDB 7D6O · PDBe 7D6O · UniProt P80457
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.