MolNFT v1 · #5326 · protein
Cholera toxin B-pentamer complexed with metanitrophenyl-alpha-D- galactose
1EEI · Protein (cholera toxin B): “Cholera toxin B-pentamer complexed with metanitrophenyl-alpha-D- galactose”. X-ray diffraction, 1 ligand (GAA), 4 pockets (best druggability 0.74). MolNFT v1 #5326 on GenesisL1: 3D structure, binding…
- PDB
- 1EEI
- Type
- protein
- Length
- 515 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (cholera toxin B)
- UniProt
- Q57193
- Ligands
- GAA
- 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 | Protein (cholera toxin B) | protein | 103 | 24% helix, 37% strand | Q57193 |
Ligands and binding sites
- GAA · 3-nitrophenyl alpha-D-galactopyranoside · 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 | 971 | 0.74 | 0.77 | 43 | empty |
| 2 | 63 | 0.40 | 0.80 | 20 | empty |
| 3 | 59 | 0.39 | 0.80 | 21 | empty |
| 4 | 59 | 0.30 | 0.75 | 11 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1329 Ų buried · 28 hydrogen bonds · protein-protein
- G–H · 1285 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1272 Ų buried · 23 hydrogen bonds · protein-protein
- F–G · 1268 Ų buried · 22 hydrogen bonds · protein-protein
- D–H · 1266 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1EEI · Cholera toxin B-pentamer complexed with metanitrophenyl-alpha-D-galactose · 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 1EEI · PDBe 1EEI · UniProt Q57193
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