MolNFT v1 · #134174 · protein
Crystal structure of N-glycan transport solute binding protein (ngts) from streptococcus pneumoniae in complex with MAN1GLCNAC
5SWA · Extracellular solute-binding protein: “Crystal structure of N-glycan transport solute binding protein (ngts) from streptococcus pneumoniae in…”. X-ray diffraction, 3 ligands (NAG, BMA, BR), 8 pockets (best druggability 0.83). MolNFT…
- PDB
- 5SWA
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein
- UniProt
- A0A0T7JX40
- Ligands
- NAG, BMA, BR
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein | protein | 448 | 39% helix, 16% strand | A0A0T7JX40 |
| B | Extracellular solute-binding protein | protein | 450 | 40% helix, 16% strand | A0A0T7JX40 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.83 | 0.84 | 108 | NAG, BMA |
| 2 | 832 | 0.82 | 0.85 | 102 | NAG, BMA |
| 3 | 50 | 0.67 | 0.96 | 21 | empty |
| 4 | 311 | 0.60 | 0.78 | 37 | empty |
| 5 | 378 | 0.59 | 0.76 | 40 | BR |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5SWA · Crystal structure of N-glycan transport solute binding protein (NgtS) from Streptococcus… · 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 A0A0T7JX40
- Elsewhere: RCSB PDB 5SWA · PDBe 5SWA · UniProt A0A0T7JX40
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