1RCV: Cholera Toxin B-Pentamer

Name: PDB 1RCV: Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1
Published: 2004-10-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1. Determined by X-ray diffraction at 1.6 Å resolution. Released 26 Oct 2004.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Vibrio cholerae
Chains: 5
Atoms: 4,668
Mol. weight: 63.78 kDa
Ligands: BV1
Released: 26 Oct 2004

Explore 1RCV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RCV 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.

Chains D and H: 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	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	5-9	5
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	61-78	18
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	5-10	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 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cholera toxin B protein (CTB)	D, E, F, G, H	protein	103	Vibrio cholerae	P01556 (AlphaFold model)

Sequence of entity 1 (D, E, F, G, H), FASTA

>1RCV_1 cholera toxin B protein (CTB) (chains D, E, F, G, H)
TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN

Ligands and cofactors

ID	Name	Formula	Copies
BV1	[3-(4-{3-[3-nitro-5-(galactopyranosyloxy)-benzoylamino]-propyl}-piperazin-1-yl)…	C50 H72 N10 O20	5

Primary citation

Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer. Pickens, J.C., Mitchell, D.D., Liu, J. et al. Chem Biol (2004) 11:1205-1215. DOI 10.1016/j.chembiol.2004.06.008 · 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
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
5ELE 1.6 Å, Cholera toxin El Tor B-pentamer in complex with A Lewis-y

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