Research workbench
Beta-glucosidase from thermotoga maritima in complex with phenethyl-substituted glucoimidazole
Analyse Beta-glucosidase from thermotoga maritima in complex with phenethyl-substituted… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CET
- Type
- protein
- Length
- 877 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase a
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- PGI, CA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase a (EC 3.2.1.21) | protein | 435 | 45% helix, 19% strand | Q08638 |
| B | Beta-glucosidase a (EC 3.2.1.21) | protein | 442 | 45% helix, 19% strand | Q08638 |
Ligands and binding sites
- PGI · (5R,6R,7S,8S)-5-(hydroxymethyl)-2-(2-phenylethyl)-1,5,6,7,8,8A-hexahydroimidazo[1,2-A] pyridine-6,7,8-triol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 675 | 0.74 | 0.80 | 57 | PGI |
| 2 | 562 | 0.72 | 0.80 | 55 | PGI |
| 3 | 54 | 0.33 | 0.76 | 10 | empty |
| 4 | 85 | 0.32 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 157 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2CET · Beta-glucosidase from Thermotoga maritima in complex with phenethyl- substituted… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · a predicted model of the same protein · chain B 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 Q08638
- Elsewhere: RCSB PDB 2CET · PDBe 2CET · UniProt Q08638
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