Research workbench
Halothermothrix orenii beta-glucosidase a, thiocellobiose complex
Analyse Halothermothrix orenii beta-glucosidase a, thiocellobiose complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PTV
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase family 1
- EC
- 3.2.1.21
- UniProt
- B8CYA8
- Ligands
- SGC, BGC, CS
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoside hydrolase family 1 (EC 3.2.1.21) | protein | 445 | 44% helix, 17% strand | B8CYA8 |
Ligands and binding sites
- SGC · 4-thio-beta-D-glucopyranose · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CS · Cesium ion · metal · 2 copies · chains A, B
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.80 | 0.91 | 41 | empty |
| 2 | 876 | 0.75 | 0.79 | 88 | SGC, BGC, PE4 |
| 3 | 567 | 0.73 | 0.80 | 42 | SGC, BGC, PE4 |
| 4 | 148 | 0.44 | 0.76 | 22 | empty |
| 5 | 78 | 0.31 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 585 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4PTV · Halothermothrix orenii beta-glucosidase A, thiocellobiose complex · the same entry in another collection · chain A 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 B8CYA8
- Elsewhere: RCSB PDB 4PTV · PDBe 4PTV · UniProt B8CYA8
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