Research workbench
Cholera toxin B-pentamer complexed with N-acyl phenyl galactoside 9H
Analyse Cholera toxin B-pentamer complexed with N-acyl phenyl galactoside 9H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PZK
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera toxin B subunit
- UniProt
- Q57193
- Ligands
- J12
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F, G, H | Cholera toxin B subunit | protein | 103 | 24% helix, 37% strand | Q57193 |
Ligands and binding sites
- J12 · N-{3-[4-(3-amino-propyl)-piperazin-1-yl]-propyl}-3-(2-thiophen-2-yl-acetylamino)-5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-yloxy)-benzamide · ligand · 5 copies · chains D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.74 | 0.77 | 41 | empty |
| 2 | 64 | 0.43 | 0.82 | 18 | empty |
| 3 | 56 | 0.34 | 0.78 | 17 | J12 |
| 4 | 50 | 0.27 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- G–H · 1328 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1303 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1295 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1291 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1281 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1PZK · Cholera Toxin B-Pentamer Complexed With N-Acyl Phenyl Galactoside 9h · the same entry in another collection · chain D against D, 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 Q57193
- Elsewhere: RCSB PDB 1PZK · PDBe 1PZK · UniProt Q57193
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