5LZJ: Cholera toxin El Tor B-pentamer

Name: PDB 5LZJ: Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237
Published: 2017-05-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237. Determined by X-ray diffraction at 1.2 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Chains: 5
Atoms: 4,898
Mol. weight: 59.77 kDa
Ligands: 7BT
Released: 31 May 2017

Explore 5LZJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LZJ 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 A: 3 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	37-41	5	1
β-strand	47-50	4	1
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain B: 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	47-49	3	1
α-helix	51-52	2
α-helix	61-78	18
α-helix	80	1
β-strand	81-88	8	1
β-strand	94-102	9	1

Chain C: 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

Chain D: 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	59-78	20
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	5-10	6
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	51-52	2
α-helix	59-78	20
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 enterotoxin subunit B	A, B, C, D, E	protein	103	Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)	P01556 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>5LZJ_1 Cholera enterotoxin subunit B (chains A, B, C, D, E)
TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN

Ligands and cofactors

ID	Name	Formula	Copies
7BT	(~{Z})-~{N}-[2-[(2~{R},3~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(ox…	C20 H29 N O9	2

Water and common crystallization additives (PGE, PEG, SO4) are not listed.

Primary citation

Towards new cholera prophylactics and treatment: Crystal structures of bacterial enterotoxins in complex with GM1 mimics. Heggelund, J.E., Mackenzie, A., Martinsen, T. et al. Sci Rep (2017) 7:2326-2326. DOI 10.1038/s41598-017-02179-0 · 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
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
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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