Research workbench
Rat xanthine oxidoreductase, D428A variant, NADH bound form
Analyse Rat xanthine oxidoreductase, D428A variant, NADH bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AD4
- Type
- protein
- Length
- 2,591 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, URC, BCT, FAD, NAI
- Pockets
- 20 · best druggability 0.90
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 | 1300 | 33% helix, 23% strand | P22985 |
| B | Xanthine DEHYDROGENASE/OXIDASE (EC 1.17.1.4, 1.17.3.2) | protein | 1291 | 33% helix, 23% strand | P22985 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
- URC · Uric acid · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · 2 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
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 | 983 | 0.90 | 0.91 | 155 | empty |
| 2 | 959 | 0.85 | 0.86 | 92 | FAD, NAI |
| 3 | 448 | 0.84 | 0.91 | 56 | empty |
| 4 | 885 | 0.83 | 0.85 | 104 | empty |
| 5 | 819 | 0.83 | 0.85 | 94 | empty |
Interfaces
1 interface between chains.
- A–B · 2718 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 6AD4 · Rat Xanthine oxidoreductase, D428A variant, NADH bound form · 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 6AD4 · PDBe 6AD4 · UniProt P22985
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