MolNFT v1 · #58635 · protein
Structure of xanthine oxidase with 2-hydroxy-6-methylpurine
3B9J: “Structure of xanthine oxidase with 2-hydroxy-6-methylpurine”. X-ray diffraction, 6 ligands (FES, FAD, MTE), 20 pockets (best druggability 0.87). MolNFT v1 #58635 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3B9J
- Type
- protein
- Length
- 2,439 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine oxidase
- EC
- 1.17.3.2
- UniProt
- P80457
- Ligands
- FES, FAD, MTE, MOS, 290, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I | Xanthine oxidase (EC 1.17.3.2) | protein | 162 | 32% helix, 18% strand | P80457 |
| B, J | Xanthine oxidase (EC 1.17.3.2) | protein | 305 | 35% helix, 23% strand | P80457 |
| C | Xanthine oxidase (EC 1.17.3.2) | protein | 758 | 32% helix, 25% strand | P80457 |
| K | Xanthine oxidase (EC 1.17.3.2) | protein | 747 | 33% helix, 26% strand | P80457 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, C, I, K
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, I, J
- 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, C, I, K
- MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains C, K
- 290 · 6-methyl-3,9-dihydro-2H-purin-2-one · ligand · 2 copies · chains C, K
- CA · Calcium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.87 | 0.88 | 97 | FAD |
| 2 | 933 | 0.85 | 0.86 | 89 | FAD |
| 3 | 1027 | 0.84 | 0.85 | 141 | empty |
| 4 | 577 | 0.82 | 0.88 | 74 | empty |
| 5 | 637 | 0.82 | 0.86 | 71 | empty |
Interfaces
9 interfaces between chains.
- C–K · 2966 Ų buried · 55 hydrogen bonds · protein-protein
- A–C · 2116 Ų buried · 32 hydrogen bonds · protein-protein
- I–K · 2115 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1420 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 1395 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3B9J · Structure of Xanthine Oxidase with 2-hydroxy-6-methylpurine · the same entry in another collection · chain K against K, TM-score 1.00
- P80457 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P80457) · 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 P80457
- Elsewhere: RCSB PDB 3B9J · PDBe 3B9J · UniProt P80457
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