MolNFT v1 · #182479 · protein
Three-dimensional structure of a GH3 beta-glucosidase from clostridium thermocellum in complex with glycerol
7MS2 · Thermostable beta-glucosidase B: “Three-dimensional structure of a GH3 beta-glucosidase from clostridium thermocellum in complex with glycerol”. X-ray diffraction, 1 ligand (CL), 12 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 7MS2
- Type
- protein
- Length
- 1,495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable beta-glucosidase B
- EC
- 3.2.1.21
- UniProt
- P14002
- Ligands
- CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable beta-glucosidase B (EC 3.2.1.21) | protein | 750 | 36% helix, 21% strand | P14002 |
| B | Thermostable beta-glucosidase B (EC 3.2.1.21) | protein | 745 | 36% helix, 21% strand | P14002 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 833 | 0.79 | 0.82 | 96 | GOL |
| 2 | 493 | 0.77 | 0.85 | 63 | GOL |
| 3 | 605 | 0.76 | 0.82 | 55 | GOL |
| 4 | 154 | 0.58 | 0.83 | 31 | BME |
| 5 | 132 | 0.57 | 0.84 | 23 | BME |
Interfaces
1 interface between chains.
- A–B · 2581 Ų buried · 51 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7MS2 · Three-dimensional structure of a GH3 Beta-glucosidase from Clostridium thermocellum in… · the same entry in another collection · chain A against A, TM-score 1.00
- P14002 · AlphaFold monomer V2.0 prediction for thermostable beta-glucosidase B (P14002) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P14002
- Elsewhere: RCSB PDB 7MS2 · PDBe 7MS2 · UniProt P14002
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