2VQ1 | pdb_00002vq1

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.260 (Depositor), 0.258 (DCC)
R-Value Work:
0.203 (Depositor), 0.202 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22356
Primary Citation 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.

Organizational Affiliation

Leiden University, The Netherlands. d.de.geus@chem.leidenuniv.nl

Macromolecule Content

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

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGKV1-117 PROTEIN	A, C [auth E]	217	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01631 (Mus musculus) Explore P01631 Go to UniProtKB: P01631
Find proteins for P01837 (Mus musculus) Explore P01837 Go to UniProtKB: P01837
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P01837 P01631
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
UniProt
Find proteins for P03987 (Mus musculus) Explore P03987 Go to UniProtKB: P03987
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain P [auth F] SDF format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain P [auth F] MOL2 format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain P [auth F] mmCIF format, chain G [auth A]	G [auth A], J [auth B], P [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain P [auth F]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth E] SDF format, chain O [auth F] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth E] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth E] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth E] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth E] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth E] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] K [auth E] L [auth E] 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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth E] Focus chain L [auth E] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth F]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.260 (Depositor), 0.258 (DCC)
R-Value Work: 0.203 (Depositor), 0.202 (DCC)
R-Value Observed: 0.206 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2009-01-27

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-11-20
Changes: Structure summary