Research workbench
Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in complex with D-glucuronic acid
Analyse Crystal structure of beta-glucuronidase from Acidobacterium capsulatum in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VNZ
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Acidobacterium capsulatum
- Molecule
- beta-GLUCURONIDASE
- EC
- 3.2.1.31
- UniProt
- C1F2K5
- Ligands
- BDP, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.8 · 1 distinct chain · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | beta-GLUCURONIDASE (EC 3.2.1.31) | protein | 466 | 30% helix, 30% strand | C1F2K5 |
Ligands and binding sites
- BDP · beta-D-glucopyranuronic acid · sugar · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.62 | 0.82 | 29 | BDP |
| 2 | 147 | 0.46 | 0.76 | 29 | empty |
| 3 | 74 | 0.38 | 0.78 | 17 | empty |
| 4 | 63 | 0.29 | 0.74 | 20 | empty |
Compared structures
- 3VNZ · Crystal structure of beta-glucuronidase from acidobacterium capsulatum in complex with… · 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 C1F2K5
- Elsewhere: RCSB PDB 3VNZ · PDBe 3VNZ · UniProt C1F2K5
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