Research workbench
Crystal structure of xanthine dehydrogenase from rhodobacter capsulatus
Analyse Crystal structure of xanthine dehydrogenase from rhodobacter capsulatus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JRO
- 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, FAD, MTE, MOS, 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 | 33% helix, 26% strand | — |
Ligands and binding sites
- FES · Fe2/s2 (inorganic) cluster · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, C, E, G
- 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
- 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 | 955 | 0.87 | 0.89 | 102 | empty |
| 2 | 1107 | 0.86 | 0.87 | 100 | empty |
| 3 | 197 | 0.82 | 0.96 | 38 | MTE, MOS |
| 4 | 1112 | 0.81 | 0.83 | 116 | FAD |
| 5 | 526 | 0.80 | 0.86 | 75 | MTE, MOS |
Interfaces
8 interfaces between chains.
- A–B · 3613 Ų buried · 57 hydrogen bonds · protein-protein
- E–F · 3605 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3599 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 3589 Ų buried · 58 hydrogen bonds · protein-protein
- F–H · 2350 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 1JRO · Crystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus · 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 1JRO · PDBe 1JRO
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