MolNFT v1 · #146123 · protein
Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop deletion
6D89 · Beta-GALACTOSIDASE/BETA-glucuronidase: “Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop deletion”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.79). MolNFT v1 #146123 on GenesisL1: 3D structure…
- PDB
- 6D89
- Type
- protein
- Length
- 2,281 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
- CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, A | Beta-GALACTOSIDASE/BETA-glucuronidase (EC 3.2.1.31) | protein | 571 | 21% helix, 33% strand | A0A174CQK8 |
| B | Beta-GALACTOSIDASE/BETA-glucuronidase (EC 3.2.1.31) | protein | 568 | 20% helix, 31% strand | A0A174CQK8 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains C, D, A, B
- CIT · Citric acid · additive · 4 copies · chains C, D, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.79 | 0.90 | 43 | empty |
| 2 | 231 | 0.74 | 0.89 | 40 | empty |
| 3 | 203 | 0.72 | 0.89 | 35 | empty |
| 4 | 67 | 0.72 | 0.97 | 19 | empty |
| 5 | 473 | 0.72 | 0.81 | 56 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2052 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2037 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 1215 Ų buried · 17 hydrogen bonds · protein-protein
- D–A · 1201 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 6D89 · Bacteroides uniformis beta-glucuronidase 1 with N-terminal loop deletion · the same entry in another collection · chain C against C, 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 6D89 · PDBe 6D89 · UniProt A0A174CQK8
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