MolNFT v1 · #103874 · protein
Halothermothrix orenii beta-glucosidase a, 2-deoxy-2-fluoro-glucose complex
4PTW · Glycoside hydrolase family 1: “Halothermothrix orenii beta-glucosidase a, 2-deoxy-2-fluoro-glucose complex”. X-ray diffraction, 1 ligand (G2F), 6 pockets (best druggability 0.80). MolNFT v1 #103874 on GenesisL1: 3D structure…
- PDB
- 4PTW
- 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
- G2F
- Pockets
- 6 · 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
- G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.80 | 0.91 | 39 | empty |
| 2 | 588 | 0.71 | 0.79 | 58 | G2F, PG4 |
| 3 | 467 | 0.71 | 0.80 | 41 | G2F |
| 4 | 220 | 0.51 | 0.76 | 30 | empty |
| 5 | 210 | 0.50 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4PTW · Halothermothrix orenii beta-glucosidase A, 2-deoxy-2-fluoro-glucose 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 4PTW · PDBe 4PTW · UniProt B8CYA8
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