MolNFT v1 · #52796 · protein
Structure of family 1 beta-glucosidase from thermotoga maritima in complex with 3-imino-2-oxa-(+)-castanospermine
2WBG · Beta-glucosidase a: “Structure of family 1 beta-glucosidase from thermotoga maritima in complex with…”. X-ray diffraction, 1 ligand (LGS), 14 pockets (best druggability 0.74). MolNFT v1 #52796 on GenesisL1: 3D structure, binding…
- PDB
- 2WBG
- Type
- protein
- Length
- 1,772 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase a
- EC
- 3.2.1.21
- UniProt
- Q08638
- Ligands
- LGS
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Beta-glucosidase a (EC 3.2.1.21) | protein | 443 | 45% helix, 18% strand | Q08638 |
Ligands and binding sites
- LGS · (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[3,4-a]pyridine-5,6,7,8-tetrol · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.74 | 0.81 | 56 | LGS |
| 2 | 586 | 0.74 | 0.81 | 58 | LGS, ACT |
| 3 | 545 | 0.74 | 0.81 | 47 | LGS |
| 4 | 580 | 0.74 | 0.81 | 57 | LGS |
| 5 | 161 | 0.43 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1231 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1181 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WBG · Structure of family 1 beta-glucosidase from Thermotoga maritima in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q08638 · AlphaFold monomer V2.0 prediction for beta-glucosidase a (Q08638) · a predicted model of the same protein · chain C 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 2WBG · PDBe 2WBG · UniProt Q08638
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