MolNFT v1 · #146094 · protein
Bacteroides uniformis beta-glucuronidase 1 bound to thiophenyl-beta-D- glucuronide
6D7F · Beta-GALACTOSIDASE/BETA-glucuronidase: “Bacteroides uniformis beta-glucuronidase 1 bound to thiophenyl-beta-D- glucuronide”. X-ray diffraction, 2 ligands (FYJ, CL), 20 pockets (best druggability 0.74). MolNFT v1 #146094 on…
- PDB
- 6D7F
- Type
- protein
- Length
- 3,474 residues
- Chains
- 6
- 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
- FYJ, CL
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Beta-GALACTOSIDASE/BETA-glucuronidase (EC 3.2.1.31) | protein | 579 | 20% helix, 33% strand | A0A174CQK8 |
Ligands and binding sites
- FYJ · phenyl 1-thio-beta-D-glucopyranosiduronic acid · ligand · 6 copies · chains A, D, B, C, E, F
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, F
- GOL · Glycerol · additive · 19 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.74 | 0.78 | 64 | GOL |
| 2 | 785 | 0.73 | 0.78 | 79 | empty |
| 3 | 888 | 0.73 | 0.77 | 71 | FYJ, GOL |
| 4 | 60 | 0.71 | 0.97 | 18 | GOL |
| 5 | 66 | 0.71 | 0.97 | 21 | GOL |
Interfaces
9 interfaces between chains.
- A–D · 2478 Ų buried · 25 hydrogen bonds · protein-protein
- B–E · 1189 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 396 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 248 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 171 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6D7F · Bacteroides uniformis beta-glucuronidase 1 bound to thiophenyl-beta-D-glucuronide · 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 6D7F · PDBe 6D7F · UniProt A0A174CQK8
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