6HJD: Cholera toxin classical B-pentamer
Cholera toxin classical B-pentamer in complex with Lewis-x. Determined by X-ray diffraction at 1.54 Å resolution. Released 14 Aug 2019.
- Method
- X-ray diffraction
- Resolution
- 1.54 Å
- Organism
- Vibrio cholerae
- Chains
- 10
- Atoms
- 9,841
- Mol. weight
- 122.67 kDa
- Ligands
- CA, BCN, FUC
- Released
- 14 Aug 2019
Explore 6HJD in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6HJD contains 44 α-helices and 60 β-strands across 10 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chains A and D: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-22 | 8 | 1 |
| β-strand | 26-30 | 5 | 1 |
| β-strand | 37-41 | 5 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-61 | 3 | |
| α-helix | 62-78 | 17 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chains B and G: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-23 | 9 | 1 |
| β-strand | 26-30 | 5 | 1 |
| β-strand | 37-41 | 5 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-78 | 20 | |
| α-helix | 80 | 1 | |
| β-strand | 81-88 | 8 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain C: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| β-strand | 15-23 | 9 | 1 |
| β-strand | 26-30 | 5 | 1 |
| β-strand | 37-41 | 5 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-77 | 19 | |
| α-helix | 80 | 1 | |
| β-strand | 81-88 | 8 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain E: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-22 | 8 | 1 |
| β-strand | 26-30 | 5 | 1 |
| β-strand | 37-41 | 5 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 61-77 | 17 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain F: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-22 | 8 | 2 |
| β-strand | 26-30 | 5 | 2 |
| β-strand | 38-41 | 4 | 2 |
| β-strand | 47-50 | 4 | 2 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-61 | 3 | |
| α-helix | 62-78 | 17 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 2 |
| β-strand | 94-101 | 8 | 2 |
Chain H: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| β-strand | 15-23 | 9 | 2 |
| β-strand | 26-30 | 5 | 2 |
| β-strand | 38-41 | 4 | 2 |
| β-strand | 47-50 | 4 | 2 |
| α-helix | 51-53 | 3 | |
| α-helix | 61-78 | 18 | |
| α-helix | 80 | 1 | |
| β-strand | 81-88 | 8 | 2 |
| β-strand | 94-102 | 9 | 2 |
Chain I: 5 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-22 | 8 | 2 |
| β-strand | 26-32 | 7 | 2 |
| β-strand | 35-41 | 7 | 2 |
| β-strand | 47-50 | 4 | 2 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-61 | 3 | |
| α-helix | 62-78 | 17 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 2 |
| β-strand | 94-102 | 9 | 2 |
Chain J: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-9 | 5 | |
| β-strand | 15-22 | 8 | 2 |
| β-strand | 26-30 | 5 | 2 |
| β-strand | 38-41 | 4 | 2 |
| β-strand | 47-50 | 4 | 2 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-78 | 20 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 2 |
| β-strand | 94-102 | 9 | 2 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cholera toxin B subunit | A, B, C, D, E, F, G, H, I, J | protein | 103 | Vibrio cholerae | P01556 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA
>6HJD_1 Cholera toxin B subunit (chains A, B, C, D, E, F, G, H, I, J)
TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| CA | Calcium ion | Ca | 10 |
| BCN | Bicine | C6 H13 N O4 | 10 |
| FUC | alpha-L-fucopyranose | C6 H12 O5 | 1 |
Primary citation
Crystal structures of cholera toxin in complex with fucosylated receptors point to importance of secondary binding site. Heim, J.B., Hodnik, V., Heggelund, J.E. et al. Sci Rep (2019) 9:12243-12243. DOI 10.1038/s41598-019-48579-2 · PubMed
Other PDB entries of the same protein (UniProt P01556 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5LZG 1.13 Å, Cholera toxin El Tor B-pentamer in complex with inhibitor PC262
- 5LZJ 1.2 Å, Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237
- 3CHB 1.25 Å, Cholera toxin B-pentamer complexed with GM1 pentasaccharide
- 1JR0 1.3 Å, Cholera toxin B-pentamer with ligand bmsc-0011
- 1RDP 1.35 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3
- 1RF2 1.35 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4
- 1RD9 1.44 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2
- 1MD2 1.45 Å, Cholera toxin B-pentamer with decavalent ligand bmsc-0013
- 5ELC 1.5 Å, Cholera toxin El Tor B-pentamer in complex with Lewis-y
- 5ELF 1.55 Å, Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide
- 1RCV 1.6 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1
- 5ELE 1.6 Å, Cholera toxin El Tor B-pentamer in complex with A Lewis-y
Browse structure collections
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