Research workbench
Crystal structure of human xanthine oxidoreductase mutant, GLU803VAL
Analyse Crystal structure of human xanthine oxidoreductase mutant, GLU803VAL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E1Q
- Type
- protein
- Length
- 5,228 residues
- Chains
- 4
- 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
- P47989
- Ligands
- FES, BCT, FAD, MTE, MOM, SAL, CA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1307 | 33% helix, 23% strand | P47989 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D
- BCT · Bicarbonate ion · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 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 · 4 copies · chains A, B, C, D
- MOM · Hydroxy(dioxo)molybdenum · ligand · 4 copies · chains A, B, C, D
- SAL · 2-hydroxybenzoic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
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 | 1125 | 0.90 | 0.91 | 172 | empty |
| 2 | 1105 | 0.85 | 0.86 | 117 | FAD |
| 3 | 884 | 0.85 | 0.87 | 87 | FAD |
| 4 | 1120 | 0.84 | 0.86 | 141 | empty |
| 5 | 1027 | 0.83 | 0.84 | 88 | FAD |
Interfaces
3 interfaces between chains.
- A–B · 2777 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 2730 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 244 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2E1Q · Crystal Structure of Human Xanthine Oxidoreductase mutant, Glu803Val · the same entry in another collection · chain A against A, TM-score 1.00
- P47989 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P47989) · 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 P47989
- Elsewhere: RCSB PDB 2E1Q · PDBe 2E1Q · UniProt P47989
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