Research workbench
Crystal structure of a rat xanthine dehydrogenase triple mutant (C535A, C992R and C1324S)
Analyse Crystal structure of a rat xanthine dehydrogenase triple mutant (C535A, C992R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WYG
- Type
- protein
- Length
- 1,297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine DEHYDROGENASE/OXIDASE
- EC
- 1.1.1.204, 1.1.3.22
- UniProt
- P22985
- Ligands
- FES, FAD, SAL, CA, PO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthine DEHYDROGENASE/OXIDASE (EC 1.1.1.204, 1.1.3.22) | protein | 1297 | 32% helix, 22% strand | P22985 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- SAL · 2-hydroxybenzoic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- ACY · Acetic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.82 | 0.83 | 90 | FAD |
| 2 | 946 | 0.81 | 0.83 | 81 | empty |
| 3 | 338 | 0.80 | 0.90 | 64 | PO4, SAL, ACY |
| 4 | 771 | 0.78 | 0.81 | 73 | empty |
| 5 | 405 | 0.76 | 0.85 | 55 | empty |
Compared structures
- 1WYG · Crystal Structure of a Rat Xanthine Dehydrogenase Triple Mutant (C535A, C992R and C1324S) · the same entry in another collection · chain A against A, TM-score 1.00
- P22985 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P22985) · 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 P22985
- Elsewhere: RCSB PDB 1WYG · PDBe 1WYG · UniProt P22985
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