1LTI

HEAT-LABILE ENTEROTOXIN (LT-I) COMPLEX WITH T-ANTIGEN

PDB DOI: https://doi.org/10.2210/pdb1LTI/pdb

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

Deposited: 1996-05-09 Released: 1996-08-17
Deposition Author(s): Van Den Akker, F., Hol, W.G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.274
R-Value Work: 0.185
R-Value Observed: 0.185

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Tumor marker disaccharide D-Gal-beta 1, 3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli.

van den Akker, F., Steensma, E., Hol, W.G.

(1996) Protein Sci 5: 1184-1188

PubMed: 8762150 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.5560050621
Primary Citation of Related Structures:
1LTI

PubMed Abstract:
Heat-labile enterotoxin (LT) is part of the cholera toxin (CT) family and consists of a catalytic A subunit and a B pentamer that serves to recognize the oligosaccharide part of the GM1 ganglioside receptor. We report here the crystal structure of heat-labile enterotoxin in complex with the disaccharide portion of the Thomsen-Friedenreich (T-antigen) tumor marker. The toxin:carbohydrate complex is determined to 2.13 A resolution, yielding an R-factor of 18.5%. The T-antigen disaccharide, D-Gal-beta 1,3-GalNAc-Ser/Thr, is present in more than 85% of human carcinomas and monitoring its autoimmune response is used for the early detection of tumors. Insight into the molecular recognition of this tumor antigen by sugar binding proteins can benefit the development of a diagnostic tool for human carcinomas as well as a T-antigen directed anticancer drug delivery system.

Organizational Affiliation

Department of Biochemistry, University of Washington, Seattle 98195, USA.

Macromolecule Content

Total Structure Weight: 87.83 kDa
Atom Count: 6,220
Modelled Residue Count: 741
Deposited Residue Count: 755
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 TYPE I	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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT LABILE ENTEROTOXIN TYPE I	F [auth A]	192	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

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT LABILE ENTEROTOXIN TYPE I	G [auth C]	48	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

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	H [auth B]	2		N/A	Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

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 J [auth E] SDF format, chain K [auth H] SDF format, chain I [auth D] MOL2 format, chain J [auth E] MOL2 format, chain K [auth H] MOL2 format, chain I [auth D]	I [auth D], J [auth E], K [auth H]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth H] Interactions & Density Focus chain I [auth D] Focus chain J [auth E] Focus chain K [auth H]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084 Query on PRD_900084	H [auth B]	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.274
R-Value Work: 0.185
R-Value Observed: 0.185
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.7	α = 90
b = 100.5	β = 90
c = 64.4	γ = 90

Software Package:

Software Name	Purpose
RAXIS	data collection
RAXIS	data reduction
X-PLOR	model building
X-PLOR	refinement
R-AXIS	data reduction
R-AXIS	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1996-08-17

Deposition Author(s):

Van Den Akker, F.

Hol, W.G.J.

Revision History (Full details and data files)

Version 1.0: 1996-08-17
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary