Research workbench
Crystal structure of a xanthine dehydrogenase (BH1974) from bacillus halodurans at 2.80 a resolution
Analyse Crystal structure of a xanthine dehydrogenase (BH1974) from bacillus halodurans… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ON5
- Type
- protein
- Length
- 659 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- BH1974 protein
- UniProt
- Q9KBF4
- Ligands
- CL
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | BH1974 protein | protein | 336 | 33% helix, 25% strand | Q9KBF4 |
| B | BH1974 protein | protein | 323 | 34% helix, 24% strand | Q9KBF4 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.74 | 0.78 | 82 | CL |
| 2 | 589 | 0.74 | 0.81 | 54 | empty |
| 3 | 610 | 0.69 | 0.78 | 56 | empty |
| 4 | 212 | 0.57 | 0.80 | 30 | empty |
| 5 | 60 | 0.41 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1888 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3ON5 · Crystal structure of a xanthine dehydrogenase (BH1974) from Bacillus halodurans at 2.80 A… · the same entry in another collection · chain B against B, 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 Q9KBF4
- Elsewhere: RCSB PDB 3ON5 · PDBe 3ON5 · UniProt Q9KBF4
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