MolNFT v1 · #151408 · protein
Cholera toxin classical B-pentamer in complex with fucosyl-GM1
6HMY · Cholera enterotoxin B-subunit: “Cholera toxin classical B-pentamer in complex with fucosyl-GM1”. X-ray diffraction, 8 ligands (BCN, GAL, FUC), 12 pockets (best druggability 0.79). MolNFT v1 #151408 on GenesisL1: 3D structure…
- PDB
- 6HMY
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera enterotoxin B-subunit
- UniProt
- Q57193
- Ligands
- BCN, GAL, FUC, NGA, SIA, BGC, GLC, CA
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cholera enterotoxin B-subunit | protein | 103 | 22% helix, 36% strand | Q57193 |
Ligands and binding sites
- BCN · Bicine · ligand · 10 copies · chains A, E, G, F, B, J, C, I, D, H
- GAL · beta-D-galactopyranose · sugar · 20 copies · chains A, B, C, D, E, F, G, H, I, J
- FUC · alpha-L-fucopyranose · sugar · 12 copies · chains A, B, C, D, E, F, G, H, I, J
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- BGC · beta-D-glucopyranose · sugar · 8 copies
- GLC · alpha-D-glucopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 10 copies · chains A, G, B, F, J, C, D, H, I, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.79 | 0.82 | 83 | CA, BCN |
| 2 | 683 | 0.78 | 0.83 | 69 | BCN, CA |
| 3 | 831 | 0.76 | 0.80 | 40 | empty |
| 4 | 813 | 0.75 | 0.80 | 39 | empty |
| 5 | 63 | 0.40 | 0.80 | 22 | empty |
Interfaces
23 interfaces between chains.
- B–C · 1333 Ų buried · 20 hydrogen bonds · protein-protein
- F–J · 1314 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 1310 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1310 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1309 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6HMY · Cholera toxin classical B-pentamer in complex with fucosyl-GM1 · the same entry in another collection · chain B against B, 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 6HMY · PDBe 6HMY · UniProt Q57193
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