MolNFT v1 · #146082 · protein
Bacteroides uniformis beta-glucuronidase 1 bound to glucuronate
6D6W · Beta-GALACTOSIDASE/BETA-glucuronidase: “Bacteroides uniformis beta-glucuronidase 1 bound to glucuronate”. X-ray diffraction, 2 ligands (GCU, CL), 20 pockets (best druggability 0.79). MolNFT v1 #146082 on GenesisL1: 3D structure…
- PDB
- 6D6W
- Type
- protein
- Length
- 2,316 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-GALACTOSIDASE/BETA-glucuronidase
- EC
- 3.2.1.31
- UniProt
- A0A174CQK8
- Ligands
- GCU, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-GALACTOSIDASE/BETA-glucuronidase (EC 3.2.1.31) | protein | 579 | 20% helix, 34% strand | A0A174CQK8 |
Ligands and binding sites
- GCU · alpha-D-glucopyranuronic acid · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.79 | 0.82 | 89 | empty |
| 2 | 897 | 0.74 | 0.78 | 56 | empty |
| 3 | 117 | 0.66 | 0.89 | 25 | GOL |
| 4 | 123 | 0.65 | 0.88 | 25 | GOL |
| 5 | 126 | 0.64 | 0.88 | 26 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 1184 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 367 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6D6W · Bacteroides uniformis beta-glucuronidase 1 bound to glucuronate · 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 A0A174CQK8
- Elsewhere: RCSB PDB 6D6W · PDBe 6D6W · UniProt A0A174CQK8
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