Research workbench
B-glucuronidase from ruminococcus gnavus in complex with D-glucaro 1, 5-lactone
Analyse B-glucuronidase from ruminococcus gnavus in complex with D-glucaro 1, 5-lactone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZ8
- Type
- protein
- Length
- 1,158 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Ligands
- GCB
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucuronidase | protein | 582 | 20% helix, 34% strand | Q6W7J7 |
| B | Beta-glucuronidase | protein | 576 | 21% helix, 35% strand | Q6W7J7 |
Ligands and binding sites
- GCB · (2S,3S,4S,5R)-3,4,5-trihydroxy-6-oxo-oxane-2-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.86 | 0.87 | 88 | empty |
| 2 | 775 | 0.73 | 0.78 | 97 | empty |
| 3 | 217 | 0.65 | 0.83 | 25 | empty |
| 4 | 309 | 0.60 | 0.78 | 36 | GCB |
| 5 | 59 | 0.59 | 0.91 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1602 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6JZ8 · b-glucuronidase from Ruminococcus gnavus in complex with D-glucaro 1,5-lactone · 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
- Every structure of UniProt Q6W7J7
- Elsewhere: RCSB PDB 6JZ8 · PDBe 6JZ8 · UniProt Q6W7J7
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