MolNFT v1 · #134175 · protein
Crystal structure of N-glycan transport solute binding protein (ngts) from streptococcus pneumoniae in complex with MAN5GLCNAC
5SWB · Extracellular solute-binding protein: “Crystal structure of N-glycan transport solute binding protein (ngts) from streptococcus pneumoniae in…”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.84).…
- PDB
- 5SWB
- Type
- protein
- Length
- 1,809 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein
- UniProt
- A0A0T7JX40
- Ligands
- MAN, NAG, BMA, CD
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Extracellular solute-binding protein | protein | 454 | 43% helix, 17% strand | A0A0T7JX40 |
| C | Extracellular solute-binding protein | protein | 451 | 43% helix, 17% strand | A0A0T7JX40 |
| D | Extracellular solute-binding protein | protein | 450 | 43% helix, 17% strand | A0A0T7JX40 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains A, C, D, G
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, D, G
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, C, D, G
- CD · Cadmium ion · metal · 34 copies · chains A, D, C, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.84 | 0.87 | 96 | NAG, BMA, MAN |
| 2 | 819 | 0.84 | 0.87 | 103 | NAG, BMA, MAN, CD |
| 3 | 807 | 0.84 | 0.87 | 107 | NAG, BMA, MAN |
| 4 | 801 | 0.84 | 0.87 | 99 | NAG, BMA, MAN |
| 5 | 824 | 0.74 | 0.78 | 73 | CD |
Interfaces
5 interfaces between chains.
- C–G · 860 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 757 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 216 Ų buried · 0 hydrogen bonds · protein-protein
- D–G · 193 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 124 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5SWB · 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 5SWB · PDBe 5SWB · UniProt A0A0T7JX40
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