MolNFT v1 · #111507 · protein
Structure of rat xanthine oxidoreductase, C-terminal deletion protein variant, NADH bound form
4YSW · Xanthine DEHYDROGENASE/OXIDASE: “Structure of rat xanthine oxidoreductase, C-terminal deletion protein variant, NADH bound form”. X-ray diffraction, 6 ligands (FES, FAD, NAI), 20 pockets (best druggability 0.89). MolNFT v1 #111507…
- PDB
- 4YSW
- Type
- protein
- Length
- 2,572 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
- P22985
- Ligands
- FES, FAD, NAI, BCT, URC, CA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1286 | 34% helix, 23% strand | P22985 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- URC · Uric acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 937 | 0.89 | 0.91 | 158 | empty |
| 2 | 437 | 0.84 | 0.91 | 60 | empty |
| 3 | 851 | 0.83 | 0.85 | 96 | empty |
| 4 | 945 | 0.83 | 0.84 | 93 | FAD, NAI |
| 5 | 1114 | 0.83 | 0.84 | 114 | empty |
Interfaces
1 interface between chains.
- A–B · 2737 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4YSW · Structure of rat xanthine oxidoreductase, C-terminal deletion protein variant, NADH bound… · 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 4YSW · PDBe 4YSW · UniProt P22985
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