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Structure of family 1 beta-glucosidase from thermotoga maritima in complex with 3-imino-2-thia-(+)- castanospermine
Analyse Structure of family 1 beta-glucosidase from thermotoga maritima 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
- 2WC4
- 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
- AMF, CA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% 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, 19% strand | Q08638 |
Ligands and binding sites
- AMF · (3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.74 | 0.81 | 56 | AMF |
| 2 | 556 | 0.74 | 0.81 | 47 | AMF |
| 3 | 620 | 0.73 | 0.80 | 52 | AMF |
| 4 | 566 | 0.73 | 0.81 | 54 | AMF |
| 5 | 153 | 0.42 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1185 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1185 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 47 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WC4 · 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 2WC4 · PDBe 2WC4 · UniProt Q08638
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