1MD2: Cholera toxin B subunit
Cholera toxin B-pentamer with decavalent ligand bmsc-0013. Determined by X-ray diffraction at 1.45 Å resolution. Released 11 Dec 2002.
- Method
- X-ray diffraction
- Resolution
- 1.45 Å
- Organism
- Vibrio cholerae
- Chains
- 5
- Atoms
- 4,967
- Mol. weight
- 60.37 kDa
- Ligands
- SQ, CYN, 233
- Released
- 11 Dec 2002
Explore 1MD2 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
1MD2 contains 20 α-helices and 30 β-strands across 5 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.
Chain D: 4 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-10 | 6 | |
| β-strand | 15-22 | 8 | 1 |
| β-strand | 26-30 | 5 | 1 |
| β-strand | 38-41 | 4 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-78 | 20 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain E: 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 | 38-41 | 4 | 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 F: 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 | 38-41 | 4 | 1 |
| β-strand | 47-50 | 4 | 1 |
| α-helix | 51-53 | 3 | |
| α-helix | 59-78 | 20 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain G: 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 | 61-78 | 18 | |
| α-helix | 80-81 | 2 | |
| β-strand | 82-88 | 7 | 1 |
| β-strand | 94-102 | 9 | 1 |
Chain H: 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 | 59-78 | 20 | |
| α-helix | 80 | 1 | |
| β-strand | 81-88 | 8 | 1 |
| β-strand | 94-102 | 9 | 1 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cholera toxin B subunit | D, E, F, G, H | protein | 103 | Vibrio cholerae | P01556 (AlphaFold model) |
Sequence of entity 1 (D, E, F, G, H), FASTA
>1MD2_1 CHOLERA TOXIN B SUBUNIT (chains D, E, F, G, H)
TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| SQ | 3-ethylamino-4-methylamino-cyclobutane-1,2-dione | C7 H12 N2 O2 | 2 |
| CYN | Cyanide ion | C N | 1 |
| 233 | [5-(3,4,5-trihydroxy-6-hydroxymethyl-tetrahydro-pyran-2-ylcarbamoyl)-pentyl]-ca… | C14 H26 N2 O8 | 5 |
Primary citation
Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin. Zhang, Z., Merritt, E.A., Ahn, M. et al. J Am Chem Soc (2002) 124:12991-12998. DOI 10.1021/ja027584k · 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
- 5ELC 1.5 Å, Cholera toxin El Tor B-pentamer in complex with Lewis-y
- 6HJD 1.54 Å, Cholera toxin classical B-pentamer in complex with Lewis-x
- 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
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