MolNFT v1 · #141509 · protein
Functional and structural characterization of a beta-glucosidase involved in saponin metabolism from intestinal bacteria
5Z9S · Glycosyl hydrolase family 3 protein: “Functional and structural characterization of a beta-glucosidase involved in saponin metabolism from…”. X-ray diffraction, 1 ligand (BGC), 20 pockets (best druggability 0.84). MolNFT v1 #141509…
- PDB
- 5Z9S
- Type
- protein
- Length
- 1,528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl hydrolase family 3 protein
- UniProt
- A0A133LV16
- Ligands
- BGC
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl hydrolase family 3 protein | protein | 765 | 30% helix, 21% strand | A0A133LV16 |
| B | Glycosyl hydrolase family 3 protein | protein | 763 | 29% helix, 21% strand | A0A133LV16 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.84 | 0.96 | 35 | empty |
| 2 | 568 | 0.66 | 0.77 | 43 | BGC |
| 3 | 469 | 0.63 | 0.76 | 59 | empty |
| 4 | 58 | 0.62 | 0.92 | 16 | empty |
| 5 | 355 | 0.61 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2993 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 5Z9S · Functional and Structural Characterization of a beta-Glucosidase Involved in Saponin… · 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 A0A133LV16
- Elsewhere: RCSB PDB 5Z9S · PDBe 5Z9S · UniProt A0A133LV16
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