MolNFT v1 · #52677 · protein
Structure of a streptococcus pneumoniae solute-binding protein in complex with the blood group a-trisaccharide.
2W7Y · Probable sugar ABC transporter, sugar-binding protein: “Structure of a streptococcus pneumoniae solute-binding protein in complex with the blood group…”. X-ray diffraction, 4 ligands (GAL, FUC, A2G), 9 pockets (best druggability…
- PDB
- 2W7Y
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable sugar ABC transporter, sugar-binding protein
- UniProt
- A5LBQ6
- Ligands
- GAL, FUC, A2G, IOD
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable sugar ABC transporter, sugar-binding protein | protein | 389 | 50% helix, 14% strand | A5LBQ6 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains A, B
- IOD · Iodide ion · ion · 2 copies · chains A, B
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 | 511 | 0.73 | 0.82 | 47 | GAL, FUC, A2G, IOD |
| 2 | 612 | 0.73 | 0.80 | 71 | GAL, FUC, A2G, IOD |
| 3 | 176 | 0.54 | 0.79 | 29 | empty |
| 4 | 84 | 0.52 | 0.84 | 20 | empty |
| 5 | 224 | 0.50 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 2W7Y · Structure of a Streptococcus pneumoniae solute-binding protein in complex with the blood… · 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 A5LBQ6
- Elsewhere: RCSB PDB 2W7Y · PDBe 2W7Y · UniProt A5LBQ6
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