1LTA

2.2 ANGSTROMS CRYSTAL STRUCTURE OF E. COLI HEAT-LABILE ENTEROTOXIN (LT) WITH BOUND GALACTOSE

PDB DOI: https://doi.org/10.2210/pdb1LTA/pdb

Classification: ENTEROTOXIN
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1993-09-15 Released: 1994-01-31
Deposition Author(s): Merritt, E.A., Sixma, T.K., Kalk, K.H., Van Zanten, B.A.M., Hol, W.G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work:
0.175 (Depositor), 0.162 (DCC)
R-Value Observed:
0.175 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Galactose-binding site in Escherichia coli heat-labile enterotoxin (LT) and cholera toxin (CT).

Merritt, E.A., Sixma, T.K., Kalk, K.H., van Zanten, B.A., Hol, W.G.

(1994) Mol Microbiol 13: 745-753

PubMed: 7997185 Search on PubMed
DOI: https://doi.org/10.1111/j.1365-2958.1994.tb00467.x
Primary Citation of Related Structures:
1LTA

PubMed Abstract:
The galactose-binding site in cholera toxin and the closely related heat-labile enterotoxin (LT) from Escherichia coli is an attractive target for the rational design of potential anti-cholera drugs. In this paper we analyse the molecular structure of this binding site as seen in several crystal structures, including that of an LT:galactose complex which we report here at 2.2 A resolution. The binding surface on the free toxin contains several tightly associated water molecules and a relatively flexible loop consisting of residues 51-60 of the B subunit. During receptor binding this loop becomes tightly ordered by forming hydrogen bonds jointly to the GM1 pentasaccharide and to a set of water molecules which stabilize the toxin:receptor complex.

Organizational Affiliation

Department of Biological Structure SM-20, University of Washington, Seattle 98195.

Macromolecule Content

Total Structure Weight: 87.52 kDa
Atom Count: 6,390
Modelled Residue Count: 748
Deposited Residue Count: 752
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT-LABILE ENTEROTOXIN, SUBUNIT B	A [auth D], B [auth E], C [auth F], D [auth G], E [auth H]	103	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P32890 (Escherichia coli) Explore P32890 Go to UniProtKB: P32890
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32890
Sequence Annotations Expand
Reference Sequence LOADING

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT-LABILE ENTEROTOXIN, SUBUNIT A	F [auth A]	188	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P06717 (Escherichia coli) Explore P06717 Go to UniProtKB: P06717
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06717
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT-LABILE ENTEROTOXIN, SUBUNIT A	G [auth C]	49	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P06717 (Escherichia coli) Explore P06717 Go to UniProtKB: P06717
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06717
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain I [auth E] SDF format, chain J [auth F] SDF format, chain K [auth G] SDF format, chain L [auth H] MOL2 format, chain H [auth D] MOL2 format, chain I [auth E] MOL2 format, chain J [auth F] MOL2 format, chain K [auth G] MOL2 format, chain L [auth H] mmCIF format, chain H [auth D] mmCIF format, chain I [auth E] mmCIF format, chain J [auth F] mmCIF format, chain K [auth G] mmCIF format, chain L [auth H]	H [auth D], I [auth E], J [auth F], K [auth G], L [auth H]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth F] Focus chain K [auth G] Focus chain L [auth H] Interactions & Density Focus chain H [auth D] Focus chain I [auth E] Focus chain J [auth F] Focus chain K [auth G] Focus chain L [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.175 (Depositor), 0.162 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.7	α = 90
b = 73.5	β = 90
c = 163.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1994-01-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1994-01-31
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary