Research workbench
B-glucuronidase from ruminococcus gnavus in complex with uronic deoxynojirimycin
Analyse B-glucuronidase from ruminococcus gnavus in complex with uronic deoxynojirimycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JZ3
- Type
- protein
- Length
- 1,159 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- UniProt
- Q6W7J7
- Ligands
- CN0
- Pockets
- 12 · 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 | 581 | 21% helix, 35% strand | Q6W7J7 |
| B | Beta-glucuronidase | protein | 578 | 21% helix, 35% strand | Q6W7J7 |
Ligands and binding sites
- CN0 · (2~{S},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl) piperidine-2-carboxylic acid · ligand · 2 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.86 | 0.87 | 81 | empty |
| 2 | 749 | 0.72 | 0.78 | 95 | empty |
| 3 | 338 | 0.60 | 0.77 | 36 | CN0 |
| 4 | 65 | 0.57 | 0.89 | 17 | empty |
| 5 | 250 | 0.55 | 0.77 | 33 | CN0 |
Interfaces
1 interface between chains.
- A–B · 1590 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6JZ3 · b-glucuronidase from Ruminococcus gnavus in complex with uronic deoxynojirimycin · 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 6JZ3 · PDBe 6JZ3 · UniProt Q6W7J7
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