MolNFT v1 · #15476 · protein
Xanthine dehydrogenase from bovine milk with inhibitor tei-6720 bound
1N5X: “Xanthine dehydrogenase from bovine milk with inhibitor tei-6720 bound”. X-ray diffraction, 5 ligands (FES, MTE, MOS), 20 pockets (best druggability 0.84). MolNFT v1 #15476 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1N5X
- Type
- protein
- Length
- 2,580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine dehydrogenase
- EC
- 1.1.1.204
- UniProt
- P80457
- Ligands
- FES, MTE, MOS, FAD, TEI
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xanthine dehydrogenase (EC 1.1.1.204) | protein | 1290 | 33% helix, 23% strand | P80457 |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains A, B
- 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 · 2 copies · chains A, B
- MOS · Dioxothiomolybdenum(vi) ion · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- TEI · 2-(3-cyano-4-isobutoxy-phenyl)-4-methyl-5-thiazole-carboxylic acid · 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 | 974 | 0.84 | 0.86 | 140 | empty |
| 2 | 986 | 0.83 | 0.84 | 93 | FAD |
| 3 | 983 | 0.83 | 0.84 | 89 | FAD |
| 4 | 881 | 0.82 | 0.85 | 83 | empty |
| 5 | 899 | 0.82 | 0.84 | 72 | empty |
Interfaces
1 interface between chains.
- A–B · 3081 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 1N5X · Xanthine Dehydrogenase from Bovine Milk with Inhibitor TEI-6720 Bound · the same entry in another collection · chain A against A, TM-score 1.00
- P80457 · AlphaFold monomer V2.0 prediction for xanthine DEHYDROGENASE/OXIDASE (P80457) · 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 P80457
- Elsewhere: RCSB PDB 1N5X · PDBe 1N5X · UniProt P80457
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