Research workbench
Salmonella typhi pltb homopentamer with neu-5NAC-9OAC-alpha-2-3-gal- beta-1-4-glcnac glycans
Analyse Salmonella typhi pltb homopentamer with neu-5NAC-9OAC-alpha-2-3-gal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TYN
- Type
- protein
- Length
- 570 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis like toxin subunit B
- UniProt
- Q8Z6A3
- Ligands
- 5N6, NAG, GAL
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Pertussis like toxin subunit B | protein | 114 | 20% helix, 42% strand | Q8Z6A3 |
Ligands and binding sites
- 5N6 · 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid · ligand · 5 copies · chains A, C, D, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, E
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.67 | 0.75 | 36 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1081 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1053 Ų buried · 27 hydrogen bonds · protein-protein
- B–E · 1051 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1045 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1017 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6TYN · Salmonella Typhi PltB Homopentamer with Neu-5NAc-9OAc-alpha-2-3-Gal-beta-1-4-GlcNAc… · 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 Q8Z6A3
- Elsewhere: RCSB PDB 6TYN · PDBe 6TYN · UniProt Q8Z6A3
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