Research workbench
Bacteroides uniformis beta-glucuronidase 2 covalently bound to cyclophellitol-6-carboxylate aziridine
Analyse Bacteroides uniformis beta-glucuronidase 2 covalently bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NZG
- Type
- protein
- Length
- 1,674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-galactosidase
- EC
- 3.2.1.23, 3.2.1.31
- UniProt
- A0A174CNH3
- Ligands
- L9D, K, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-galactosidase (EC 3.2.1.23, 3.2.1.31) | protein | 837 | 16% helix, 41% strand | A0A174CNH3 |
Ligands and binding sites
- L9D · (1S,2R,3S,4S,5S,6R)-2-amino-3,4,5,6-tetrahydroxycyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.84 | 0.87 | 87 | empty |
| 2 | 515 | 0.83 | 0.90 | 55 | empty |
| 3 | 582 | 0.81 | 0.86 | 81 | empty |
| 4 | 332 | 0.76 | 0.87 | 52 | empty |
| 5 | 196 | 0.69 | 0.87 | 36 | GOL |
Interfaces
1 interface between chains.
- A–B · 3425 Ų buried · 69 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6NZG · Bacteroides uniformis beta-glucuronidase 2 covalently bound to… · 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 A0A174CNH3
- Elsewhere: RCSB PDB 6NZG · PDBe 6NZG · UniProt A0A174CNH3
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