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The complex structure of 6-phospho-beta-glucosidase bgla-2 with thiocellobiose-6P from streptococcus pneumoniae
Analyse The complex structure of 6-phospho-beta-glucosidase bgla-2 with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IPN
- Type
- protein
- Length
- 920 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-glucosidase
- EC
- 3.2.1.86
- UniProt
- Q97S37
- Ligands
- SGC, RTG
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 457 | 43% helix, 16% strand | Q97S37 |
| E | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 463 | 41% helix, 16% strand | Q97S37 |
Ligands and binding sites
- SGC · 4-thio-beta-D-glucopyranose · ligand · 2 copies · chains B, E
- RTG · 6-O-phosphono-alpha-L-idopyranose · ligand · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.84 | 0.97 | 27 | empty |
| 2 | 422 | 0.66 | 0.78 | 34 | SGC, RTG |
| 3 | 423 | 0.65 | 0.78 | 45 | SGC, RTG |
| 4 | 70 | 0.51 | 0.85 | 16 | empty |
| 5 | 70 | 0.51 | 0.85 | 16 | empty |
Interfaces
1 interface between chains.
- B–E · 1752 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4IPN · The complex structure of 6-phospho-beta-glucosidase BglA-2 with thiocellobiose-6P from… · the same entry in another collection · chain B against B, 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 Q97S37
- Elsewhere: RCSB PDB 4IPN · PDBe 4IPN · UniProt Q97S37
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