Research workbench
Salmonella typhi pltb homopentamer with NEU5AC-alpha-2-3-gal-beta-1-4- glcnac glycans
Analyse Salmonella typhi pltb homopentamer with NEU5AC-alpha-2-3-gal-beta-1-4- glcnac… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P4M
- Type
- protein
- Length
- 570 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pertussis-like toxin subunit
- UniProt
- Q8Z6A3
- Ligands
- NAG, GAL, SIA
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Putative pertussis-like toxin subunit | protein | 114 | 20% helix, 42% strand | Q8Z6A3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D, E
- GAL · beta-D-galactopyranose · sugar · 9 copies · chains A, B, C, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 9 copies · chains A, B, 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 | 822 | 0.69 | 0.75 | 40 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1098 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1068 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1062 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1028 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1024 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 6P4M · Salmonella typhi PltB Homopentamer with Neu5Ac-alpha-2-3-Gal-beta-1-4-GlcNAc Glycans · 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 6P4M · PDBe 6P4M · UniProt Q8Z6A3
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