MolNFT v1 · #151287 · protein
Cholera toxin classical B-pentamer in complex with lewis-X
6HJD · Cholera toxin B subunit: “Cholera toxin classical B-pentamer in complex with lewis-X”. X-ray diffraction, 6 ligands (BCN, FUC, GAL), 9 pockets (best druggability 0.78). MolNFT v1 #151287 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6HJD
- Type
- protein
- Length
- 1,030 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cholera toxin B subunit
- UniProt
- D6R7L2
- Ligands
- BCN, FUC, GAL, NDG, NAG, CA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Cholera toxin B subunit | protein | 103 | 23% helix, 37% strand | D6R7L2 |
Ligands and binding sites
- BCN · Bicine · ligand · 10 copies · chains A, E, G, B, C, J, D, H, I, F
- FUC · alpha-L-fucopyranose · sugar · 9 copies · chains A, E, B, C, D, F, G, H, I, J
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains A, B, C, D, E, G, H, I
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains A, E, B, C, D, F, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, C, D, E
- CA · Calcium ion · metal · 10 copies · chains A, G, B, F, J, C, I, D, H, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.78 | 0.85 | 70 | BCN, CA |
| 2 | 541 | 0.77 | 0.84 | 59 | CA, BCN |
| 3 | 876 | 0.75 | 0.79 | 44 | empty |
| 4 | 1099 | 0.74 | 0.77 | 45 | empty |
| 5 | 198 | 0.66 | 0.85 | 30 | CA, BCN |
Interfaces
21 interfaces between chains.
- H–I · 1381 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1336 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 1323 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1323 Ų buried · 22 hydrogen bonds · protein-protein
- A–E · 1304 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 6HJD · Cholera toxin classical B-pentamer in complex with Lewis-x · the same entry in another collection · chain F against F, 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 D6R7L2
- Elsewhere: RCSB PDB 6HJD · PDBe 6HJD · UniProt D6R7L2
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