MolNFT v1 · #112541 · protein
Crystal structure of beta-glucosidase from listeria innocua in complex with gluconolactone
4ZOB · LIN1840 protein: “Crystal structure of beta-glucosidase from listeria innocua in complex with gluconolactone”. X-ray diffraction, 3 ligands (LGC, MG, SO4), 14 pockets (best druggability 0.87). MolNFT v1 #112541 on GenesisL1: 3D…
- PDB
- 4ZOB
- Type
- protein
- Length
- 1,443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN1840 protein
- UniProt
- Q92AS9
- Ligands
- LGC, MG, SO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN1840 protein | protein | 722 | 34% helix, 20% strand | Q92AS9 |
| B | LIN1840 protein | protein | 721 | 34% helix, 20% strand | Q92AS9 |
Ligands and binding sites
- LGC · D-glucono-1,5-lactone · ligand · 5 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.87 | 0.94 | 65 | PEG |
| 2 | 321 | 0.66 | 0.81 | 36 | empty |
| 3 | 317 | 0.66 | 0.81 | 36 | empty |
| 4 | 274 | 0.64 | 0.81 | 30 | GOL |
| 5 | 267 | 0.62 | 0.80 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2952 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 4ZOB · Crystal Structure of beta-glucosidase from Listeria innocua in complex with gluconolactone · 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 Q92AS9
- Elsewhere: RCSB PDB 4ZOB · PDBe 4ZOB · UniProt Q92AS9
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