5G3L

ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER COMPLEXED WITH SIALYLATED SUGAR

• PDB DOI: https://doi.org/10.2210/pdb5G3L/pdb

• Classification: TOXIN
• Organism(s): Escherichia coli HB101
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-04-29 Released: 2016-09-14 
• Deposition Author(s): Zalem, D., Benktander, J., Ribeiro, J.P., Varrot, A., Lebens, M., Imberty, A., Teneberg, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

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)

Macromolecule Content

• Total Structure Weight: 56.06 kDa 
• Atom Count: 4,495 
• Modelled Residue Count: 495 
• Deposited Residue Count: 495 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT-LABILE ENTEROTOXIN IIB, B CHAIN	A [auth D], B [auth E], E [auth H]	99	Escherichia coli HB101	Mutation(s): 0
UniProt
Find proteins for P43529 (Escherichia coli) Explore P43529  Go to UniProtKB:  P43529

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT-LABILE ENTEROTOXIN IIB, B CHAIN	C [auth F], D [auth G]	99	Escherichia coli HB101	Mutation(s): 0
UniProt
Find proteins for P43529 (Escherichia coli) Explore P43529  Go to UniProtKB:  P43529

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	F [auth A], G [auth B], H [auth C]	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	K [auth E], M [auth G]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
NA	I [auth D], J [auth E], L [auth G], N [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ME0	A [auth D], B [auth E], E [auth H]	L-PEPTIDE LINKING	C5 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.197 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.564	α = 90
b = 68.015	β = 90
c = 154.513	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Zalem, D., Benktander, J., Ribeiro, J.P., Varrot, A., Lebens, M., Imberty, A., Teneberg, S.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-11-09
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary