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The crystal structure of 6-P-beta-D-glucosidase (E375Q mutant) from streptococcus mutans UA150 in complex with gentiobiose 6-phosphate.
Analyse The crystal structure of 6-P-beta-D-glucosidase (E375Q mutant) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GPN
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-D-glucosidase
- EC
- 3.2.1.86
- UniProt
- Q8DT00
- Ligands
- BGC, BG6
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phospho-beta-D-glucosidase (EC 3.2.1.86) | protein | 478 | 41% helix, 16% strand | Q8DT00 |
| B | 6-phospho-beta-D-glucosidase (EC 3.2.1.86) | protein | 476 | 41% helix, 16% strand | Q8DT00 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.84 | 0.96 | 36 | empty |
| 2 | 642 | 0.75 | 0.81 | 49 | BGC, BG6 |
| 3 | 604 | 0.74 | 0.81 | 48 | BGC, BG6 |
| 4 | 56 | 0.68 | 0.96 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1879 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4GPN · The crystal structure of 6-P-beta-D-Glucosidase (E375Q mutant) from Streptococcus mutans… · 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 Q8DT00
- Elsewhere: RCSB PDB 4GPN · PDBe 4GPN · UniProt Q8DT00
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