1S3K

Crystal Structure of a Humanized Fab (hu3S193) in Complex with the Lewis Y Tetrasaccharide

PDB DOI: https://doi.org/10.2210/pdb1S3K/pdb

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

Deposited: 2004-01-13 Released: 2004-07-13
Deposition Author(s): Ramsland, P.A., Farrugia, W., Bradford, T.M., Hogarth, P.M., Scott, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238
R-Value Work: 0.203
R-Value Observed: 0.203

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structural convergence of antibody binding of carbohydrate determinants in lewis y tumor antigens

Ramsland, P.A., Farrugia, W., Bradford, T.M., Hogarth, P.M., Scott, A.M.

(2004) J Mol Biol 340: 809-818

PubMed: 15223322 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2004.05.037
Primary Citation of Related Structures:
1S3K

PubMed Abstract:
Antibodies targeting human epithelial carcinomas bearing Lewis Y (Le(y)) carbohydrate antigens provide a striking illustration of convergent immune recognition. We report a 1.9A resolution crystal structure of the Fab of a humanized antibody (hu3S193) in complex with the Le(y) tetrasaccharide, Fuc(alpha 1-->2)Gal(beta 1-->4)[Fuc(alpha 1-->3)]GlcNAc. Comparisons of the hu3S193 and BR96 antibodies bound to Le(y) tumor antigens revealed extremely similar mechanisms for recognition of the carbohydrate epitopes. Solvent plays a critical role in hu3S193 antibody binding to the Le(y) carbohydrate epitope. Specificity for Le(y) is maintained because a conserved pocket accepts an N-acetyl group of the core Gal(beta 1-->4)GlcNAc disaccharide. Closely related blood-group determinants (Le(a) and Le(b)) cannot enter the specificity pocket, making the Le(y) antibodies promising candidates for immunotherapy of epithelial cancer.

Organizational Affiliation

Structural Immunology Laboratory, Austin Research Institute, Heidelberg, Vic. 3084, Australia. p.ramsland@ari.unimelb.edu.au

Macromolecule Content

Total Structure Weight: 48.63 kDa
Atom Count: 3,679
Modelled Residue Count: 428
Deposited Residue Count: 441
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HU3S193 Fab fragment, light chain	A [auth L]	219	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HU3S193 Fab fragment, heavy chain	B [auth H]	222	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose	C [auth A]	4		N/A	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G82236PZ GlyCosmos: G82236PZ GlyGen: G82236PZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth L] MOL2 format, chain D [auth L]	D [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Interactions & Density Focus chain D [auth L]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900124 Query on PRD_900124	C [auth A]	Lewis Y antigen, alpha anomer	Oligosaccharide / Antigen		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.238
R-Value Work: 0.203
R-Value Observed: 0.203
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.758	α = 90
b = 71.758	β = 90
c = 90.142	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-07-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-07-13
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2020-01-01
Changes: Data collection, Derived calculations, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary