Research workbench
Crystal structure of bacteroides uniformis beta-glucuronidase
Analyse Crystal structure of bacteroides uniformis beta-glucuronidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UJ6
- Type
- protein
- Length
- 1,678 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolases family 2, sugar binding domain protein
- UniProt
- A0A078SUX9
- Ligands
- CA, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolases family 2, sugar binding domain protein | protein | 838 | 16% helix, 41% strand | A0A078SUX9 |
| B | Glycosyl hydrolases family 2, sugar binding domain protein | protein | 840 | 16% helix, 41% strand | A0A078SUX9 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 775 | 0.84 | 0.87 | 88 | empty |
| 2 | 806 | 0.82 | 0.85 | 86 | empty |
| 3 | 569 | 0.81 | 0.87 | 75 | GOL |
| 4 | 371 | 0.77 | 0.87 | 52 | GOL |
| 5 | 191 | 0.69 | 0.87 | 39 | GOL |
Interfaces
1 interface between chains.
- A–B · 3479 Ų buried · 74 hydrogen bonds · protein-protein
Compared structures
- 5UJ6 · Crystal Structure of Bacteroides Uniformis beta-glucuronidase · 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 A0A078SUX9
- Elsewhere: RCSB PDB 5UJ6 · PDBe 5UJ6 · UniProt A0A078SUX9
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