2VQ1

anti trimeric Lewis X Fab54-5C10-A

• PDB DOI: https://doi.org/10.2210/pdb2VQ1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2008-03-10 Released: 2009-01-27 
• Deposition Author(s): de Geus, D.C., van Roon, A.M.M., Thomassen, E.A.J., Hokke, C.H., Deelder, A.M., Abrahams, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Characterization of a Diagnostic Fab Fragment Binding Trimeric Lewis X.

De Geus, D.C., Van Roon, A.M.M., Thomassen, E.A.J., Hokke, C.H., Deelder, A.M., Abrahams, J.P.

(2009) Proteins 76: 439

• PubMed: 19173313 
• DOI: https://doi.org/10.1002/prot.22356
• Primary Citation of Related Structures:  
  2VQ1


• PubMed Abstract: 
  

  Lewis X trisaccharides normally function as essential cell-cell interaction mediators. However, oligomers of Lewis X trisaccharides expressed by the parasite Schistosoma mansoni seem to be related to its evasion of the immune response of its human host. Here we show that monoclonal antibody 54-5C10-A, which is used to diagnose schistosomiasis in humans, interacts with oligomers of at least three Lewis X trisaccharides, but not with monomeric Lewis X. We describe the sequence and the 2.5 A crystal structure of its Fab fragment and infer a possible mode of binding of the polymeric Lewis X from docking studies. Our studies indicate a radically different mode of binding compared to Fab 291-2G3-A, which is specific for monomeric Lewis X, thus providing a structural explanation of the diagnostic success of 54-5C10-A.

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Organizational Affiliation: 

Leiden University, The Netherlands. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 95.7 kDa 
• Atom Count: 6,868 
• Modelled Residue Count: 858 
• Deposited Residue Count: 870 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGKV1-117 PROTEIN	A, C [auth E]	217	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTI-HUMAN FC GAMMA RECEPTOR III 3G8 GAMMA HEAVY CHAIN VARIABLE REGION	B, D [auth F]	218	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], J [auth B], P [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GLY	E [auth A], F [auth A], I [auth B], K [auth E], L [auth E], M [auth E], N [auth F], O [auth F]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
AZI	H [auth A]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.260 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.384	α = 90
b = 161.015	β = 103.07
c = 53.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): de Geus, D.C., van Roon, A.M.M., Thomassen, E.A.J., Hokke, C.H., Deelder, A.M., Abrahams, J.P.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-06-23
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description