5LZI: Porcine heat-labile enterotoxin R13H

Name: PDB 5LZI: Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146
Published: 2017-05-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Porcine heat-labile enterotoxin R13H in complex with inhibitor MM146. Determined by X-ray diffraction at 1.6 Å resolution. Released 31 May 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Escherichia coli
Chains: 5
Atoms: 5,453
Mol. weight: 63.38 kDa
Ligands: PO4, 7DB, 7BQ
Released: 31 May 2017

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

Secondary structure: helices and β-sheets

5LZI 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 A and D: 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 B: 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	51-53	3
α-helix	61-77	17
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain C: 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	59-77	19
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	15-22	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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat-labile enterotoxin B chain	A, B, C, D, E	protein	103	Escherichia coli	P32890 (AlphaFold model)

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

>5LZI_1 Heat-labile enterotoxin B chain (chains A, B, C, D, E)
APQTITELCSEYHNTQIYTINDKILSYTESMAGKREMVIITFKSGETFQVEVPGSQHIDS
QKKAIERMKDTLRITYLTETKIDKLCVWNNKTPNSIAAISMKN

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
7DB	(2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{S})-3-[2-[(2~{S},3~{R},4~{R},5~…	C32 H46 N6 O15	4
7BQ	(2~{R},4~{S},5~{R},6~{R})-5-acetamido-2-[4-[(2~{R})-3-[2-[(2~{S},3~{R},4~{R},5~…	C32 H46 N6 O15	1

Water and common crystallization additives (PEG, GOL) 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 P32890 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1DJR 1.3 Å, Heat-labile enterotoxin B-pentamer complexed with M-carboxyphenyl-alpha-D-galactose
6IAL 1.45 Å, Porcine E.coli heat-labile enterotoxin B-pentamer in complex with Lacto-N-neohexaose
1EFI 1.6 Å, Heat-labile enterotoxin B-pentamer complexed with para-aminophenyl-alpha-D-galactopyranos…
1LT5 1.7 Å, Heat-labile enterotoxin B-pentamer complexed with thiodigalactoside
1EEF 1.8 Å, Heat-labile enterotoxin B-pentamer complexed with bound ligand pepg
1FD7 1.8 Å, Heat-labile enterotoxin B-pentamer with bound ligand BMSC001
2XRS 1.81 Å, Crystal structures exploring the origins of the broader specificity of escherichia coli…
1LTS 1.95 Å, Refined structure of E. Coli heat labile enterotoxin, a close relative of cholera toxin
1PZI 1.99 Å, Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Galactoside 2a
1LT3 2.0 Å, Heat-labile enterotoxin double mutant N40C/G166C
1LT4 2.0 Å, Heat-labile enterotoxin mutant S63K
1LTI 2.13 Å, Heat-labile enterotoxin (lt-I) complex with T-antigen

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