Research workbench
Cholera toxin B-pentamer with ligand bmsc-0012
Analyse Cholera toxin B-pentamer with ligand bmsc-0012 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LLR
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera toxin B subunit
- Ligands
- FNG, LNQ
- 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 | — |
Ligands and binding sites
- FNG · 5-aminocarbonyl-3-nitrophenyl alpha-D-galactopyranoside · ligand · 5 copies · chains D, E, F, G, H
- LNQ · 3-amino-4-{3-[2-(2-propoxy-ethoxy)-ethoxy]-propylamino}-cyclobut-3-ene-1,2-dione · 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 | 1006 | 0.74 | 0.77 | 42 | empty |
| 2 | 55 | 0.45 | 0.84 | 18 | empty |
| 3 | 55 | 0.38 | 0.81 | 21 | empty |
| 4 | 50 | 0.28 | 0.75 | 11 | FNG |
Interfaces
5 interfaces between chains.
- G–H · 1334 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1333 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1320 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1312 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1288 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1LLR · Cholera toxin B-pentamer with ligand bmsc-0012 · 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
- Elsewhere: RCSB PDB 1LLR · PDBe 1LLR
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