7PRS

Crystal Structure of the B subunit of heat labile enterotoxin LT-IIc from Escherichia coli in complex with Sialyl-lacto-N-neotetraose d

• PDB DOI: https://doi.org/10.2210/pdb7PRS/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-09-22 Released: 2022-02-02 
• Deposition Author(s): Varrot, A.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 119.97 kDa 
• Atom Count: 8,462 
• Modelled Residue Count: 990 
• Deposited Residue Count: 1,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat-labile enterotoxin IIA, B chain	A [auth DDD], B [auth EEE], C [auth FFF], D [auth GGG], E [auth HHH], F [auth III], G [auth JJJ], H [auth KKK], I [auth LLL], J [auth MMM]	104	Escherichia coli	Mutation(s): 0  Gene Names: LT-IIc1 B, GQM13_12885, HVV37_03950, HVV78_10285, HVW37_13205
UniProt
Find proteins for H6W8F2 (Escherichia coli) Explore H6W8F2  Go to UniProtKB:  H6W8F2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	K [auth DaD]	5		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	L [auth GaG], N [auth JaJ]	4		N/A
Glycosylation Resources
GlyTouCan:  G69440RD GlyCosmos:  G69440RD GlyGen:  G69440RD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth HaH]	3		N/A
Glycosylation Resources
GlyTouCan:  G00065MO GlyCosmos:  G00065MO GlyGen:  G00065MO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA (Subject of Investigation/LOI)	S [auth III], T [auth JJJ], U [auth KKK], V [auth LLL]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
SO4	O [auth DDD], P [auth EEE], Q [auth FFF], R [auth HHH]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.09	α = 90
b = 121.269	β = 90
c = 126.732	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-02 
Deposition Author(s): Varrot, A.

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Funding Organization	Location	Grant Number
European Commission	European Union	653706

Revision History  

• Version 1.0: 2022-02-02
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description