Research workbench
Cholera toxin B-pentamer complexed with nitrophenyl galactoside 5
Analyse Cholera toxin B-pentamer complexed with nitrophenyl galactoside 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PZJ
- 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
- 15B, J15
- Pockets
- 6 · best druggability 0.75
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
- 15B · N-{3-[4-(3-amino-propyl)-piperazin-1-yl]-propyl}-3-nitro-5-(galactopyranosyl)-beta-benzamide · ligand · 3 copies · chains D, E, G, H
- J15 · N-{3-[4-(3-amino-propyl)-piperazin-1-yl]-propyl}-3-nitro-5-(galactopyranosyl)-alpha-benzamide · ligand · 2 copies · chains E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.75 | 0.77 | 43 | empty |
| 2 | 57 | 0.42 | 0.82 | 20 | empty |
| 3 | 61 | 0.39 | 0.80 | 18 | empty |
| 4 | 60 | 0.38 | 0.80 | 18 | empty |
| 5 | 58 | 0.30 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- G–H · 1316 Ų buried · 25 hydrogen bonds · protein-protein
- F–G · 1307 Ų buried · 23 hydrogen bonds · protein-protein
- D–H · 1305 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1299 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1274 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1PZJ · Cholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5 · 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 1PZJ · PDBe 1PZJ · UniProt Q57193
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