Research workbench
Crystal structure of beta-glucosidase from listeria innocua in complex with glucose
Analyse Crystal structure of beta-glucosidase from listeria innocua in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZOD
- Type
- protein
- Length
- 1,441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN1840 protein
- UniProt
- Q92AS9
- Ligands
- BGC, MG, SO4
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN1840 protein | protein | 720 | 34% helix, 20% strand | Q92AS9 |
| B | LIN1840 protein | protein | 721 | 35% helix, 20% strand | Q92AS9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · 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 | 491 | 0.87 | 0.94 | 69 | GOL |
| 2 | 333 | 0.68 | 0.82 | 35 | empty |
| 3 | 299 | 0.66 | 0.82 | 34 | empty |
| 4 | 294 | 0.64 | 0.80 | 34 | GOL |
| 5 | 275 | 0.63 | 0.81 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 2906 Ų buried · 77 hydrogen bonds · protein-protein
Compared structures
- 4ZOD · Crystal Structure of beta-glucosidase from Listeria innocua in complex with glucose · the same entry in another collection · chain B against B, 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 4ZOD · PDBe 4ZOD · UniProt Q92AS9
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