Research workbench
Cholera toxin B subunit with attached SIV epitope
Analyse Cholera toxin B subunit with attached SIV epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LVB
- Type
- protein
- Length
- 1,073 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin B-SUBUNIT,SURFACE protein GP120
- UniProt
- Q57193
- Ligands
- GAL, CL
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, G, H, C, I, J | Cholera enterotoxin B-SUBUNIT,SURFACE protein GP120 | protein | 107 | 23% helix, 34% strand | Q57193 |
| F, A, B | Cholera enterotoxin B-SUBUNIT,SURFACE protein GP120 | protein | 108 | 24% helix, 33% strand | Q57193 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 10 copies · chains D, E, F, G, H, A, B, C, I, J
- CL · Chloride ion · ion · 11 copies · chains D, E, G, F, H, A, B, C, I, J
- PGE · Triethylene glycol · additive · 15 copies · chains D, E, H, F, G, A, B, C, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.76 | 0.79 | 38 | empty |
| 2 | 1079 | 0.74 | 0.77 | 44 | empty |
| 3 | 55 | 0.43 | 0.83 | 18 | empty |
| 4 | 63 | 0.41 | 0.81 | 20 | empty |
| 5 | 58 | 0.40 | 0.81 | 20 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1387 Ų buried · 24 hydrogen bonds · protein-protein
- D–H · 1384 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1382 Ų buried · 25 hydrogen bonds · protein-protein
- A–J · 1379 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1372 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 7LVB · Cholera toxin B subunit with attached SIV epitope · 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 7LVB · PDBe 7LVB · UniProt Q57193
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