Research workbench
Crystal structure of beta-glucuronidase from acidobacterium capsulatum covalent-bonded with 2-deoxy-2-fluoro-D-glucuronic acid
Analyse Crystal structure of beta-glucuronidase from acidobacterium capsulatum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VO0
- Type
- protein
- Length
- 466 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucuronidase
- EC
- 3.2.1.31
- UniProt
- C1F2K5
- Ligands
- DNF, GUF, GUZ, PO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 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
- DNF · 2,4-dinitrophenol · ligand · 3 copies · chains A
- GUF · 2-deoxy-2-fluoro-beta-D-glucopyranuronic acid · ligand · 2 copies · chains A
- GUZ · 2-deoxy-2-fluoro-alpha-D-glucopyranuronic acid · ligand · chains A
- PO4 · Phosphate ion · ion · 2 copies · 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 | 228 | 0.61 | 0.81 | 31 | GUZ, DNF |
| 2 | 153 | 0.47 | 0.77 | 34 | empty |
| 3 | 105 | 0.39 | 0.76 | 25 | empty |
| 4 | 67 | 0.29 | 0.74 | 18 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3VO0 · Crystal structure of beta-glucuronidase from Acidobacterium capsulatum covalent-bonded… · 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 3VO0 · PDBe 3VO0 · UniProt C1F2K5
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