MolNFT v1 · #111545 · protein
Rat xanthine oxidoreductase, C-terminal deletion protein variant, crystal grown without dithiothreitol
4YTZ · Xanthine DEHYDROGENASE/OXIDASE: “Rat xanthine oxidoreductase, C-terminal deletion protein variant, crystal grown without dithiothreitol”. X-ray diffraction, 5 ligands (FES, FAD, URC), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 4YTZ
- Type
- protein
- Length
- 2,562 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, URC, BCT, CA
- Pockets
- 20 · best druggability 0.89
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 | 1289 | 34% helix, 23% strand | P22985 |
| B | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1273 | 33% 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
- URC · Uric acid · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.89 | 0.90 | 116 | FAD |
| 2 | 1014 | 0.88 | 0.89 | 95 | FAD |
| 3 | 1200 | 0.85 | 0.86 | 139 | empty |
| 4 | 1175 | 0.84 | 0.85 | 136 | empty |
| 5 | 524 | 0.81 | 0.87 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 2778 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4YTZ · Rat xanthine oxidoreductase, C-terminal deletion protein variant, crystal grown without… · 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 0.99
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 4YTZ · PDBe 4YTZ · UniProt P22985
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