MolNFT v1 · #11608 · protein
Crystal structure of xanthine dehydrogenase inhibited by alloxanthine from rhodobacter capsulatus
1JRP · Xanthine dehydrogenase, chain a: “Crystal structure of xanthine dehydrogenase inhibited by alloxanthine from rhodobacter capsulatus”. X-ray diffraction, 6 ligands (FES, MTE, MOS), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 1JRP
- Type
- protein
- Length
- 4,840 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthine dehydrogenase, chain a; Xanthine dehydrogenase, chain B
- EC
- 1.1.1.204
- Ligands
- FES, MTE, MOS, FAD, 141, CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Xanthine dehydrogenase, chain a (EC 1.1.1.204) | protein | 450 | 36% helix, 22% strand | — |
| B, D, F, H | Xanthine dehydrogenase, chain B (EC 1.1.1.204) | protein | 760 | 32% helix, 26% strand | — |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 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 · 4 copies · chains A, B, C, D, E, F, G, H
- MOS · Dioxothiomolybdenum(vi) ion · ligand · 4 copies · chains B, D, F, H
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, E, G
- 141 · Oxypurinol · ligand · 4 copies · chains B, D, F, H
- CA · Calcium ion · metal · 4 copies · chains B, D, F, H
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 | 1017 | 0.87 | 0.88 | 84 | empty |
| 2 | 1186 | 0.86 | 0.87 | 119 | empty |
| 3 | 773 | 0.82 | 0.85 | 77 | FAD |
| 4 | 524 | 0.80 | 0.87 | 77 | MTE, MOS, 141 |
| 5 | 522 | 0.80 | 0.86 | 76 | MTE, MOS, 141 |
Interfaces
8 interfaces between chains.
- E–F · 3609 Ų buried · 64 hydrogen bonds · protein-protein
- A–B · 3591 Ų buried · 55 hydrogen bonds · protein-protein
- G–H · 3583 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3559 Ų buried · 53 hydrogen bonds · protein-protein
- F–H · 2355 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1JRP · Crystal Structure of Xanthine Dehydrogenase inhibited by alloxanthine from Rhodobacter… · the same entry in another collection · 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
- Elsewhere: RCSB PDB 1JRP · PDBe 1JRP
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