Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 48.54 kDa 
• Atom Count: 3395 
• Modelled Residue Count: 436 
• Deposited Residue Count: 438 
• Unique protein chains: 2

1CLY

IGG FAB (HUMAN IGG1, KAPPA) CHIMERIC FRAGMENT (CBR96) COMPLEXED WITH LEWIS Y NONOATE METHYL ESTER

• PDB DOI: 10.2210/pdb1CLY/pdb

• Classification: IMMUNOGLOBULIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1995-03-15 Released: 1996-08-01 
• Deposition Author(s): Sheriff, S., Bajorath, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 

Literature

The x-ray structure of an anti-tumour antibody in complex with antigen.

Jeffrey, P.D., Bajorath, J., Chang, C.Y., Yelton, D., Hellstrom, I., Hellstrom, K.E., Sheriff, S.

(1995) Nat Struct Biol 2: 466-471

• PubMed: 7664109 
• DOI: 10.1038/nsb0695-466
• Primary Citation of Related Structures:  
  1CLY, 1CLZ


• PubMed Abstract: 
  

The crystal structures of the murine BR96 Fab and its human chimera have been determined in complex with the nonoate methyl ester derivative of Lewis Y (nLey) at 2.8 A and 2.5 A resolution, respectively. BR96 binds the carbohydrate in a large pocket which is formed by residues of all CDR loops except L2. The binding of the carbohydrate is mediated predominantly by aromatic residues in BR96. Analysis of the structure suggests that BR96 is capable of recognizing a structure larger than the Le(y) tetrasaccharide, providing a possible explanation for its high tumour selectivity. The structure provides a rationale for mutagenesis experiments that have resulted in BR96 CDR loop mutants with increased affinity for nLey and/or tumour cells.

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Related Citations: 

• Crystallization and Preliminary X-Ray Analysis of the Monoclonal Anti-Tumor Antibody Br96 and its Complex with the Lewis Y Determinant
  Chang, C.Y., Jeffrey, P.D., Bajorath, J., Hellstrom, I., Hellstrom, K.E., Sheriff, S.
  (1994) J Mol Biol 235: 372

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Organizational Affiliation: 

Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08543-4000, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG FAB (HUMAN IGG1, KAPPA)	A [auth L]	219	Homo sapiens	Mutation(s): 0  Gene Names: IGKC
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IGG FAB (HUMAN IGG1, KAPPA)	B [auth H]	219	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	4		N/A
Glycosylation Resources
GlyTouCan:  G00052MO GlyCosmos:  G00052MO GlyGen:  G00052MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NON	D [auth H]	METHYL NONANOATE (ESTER) C10 H20 O2 IJXHLVMUNBOGRR-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900054	C [auth A]	Lewis Y antigen, beta anomer	Oligosaccharide / Antigen		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.298 
• R-Value Work: 0.238 
• R-Value Observed: 0.238 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.7	α = 90
b = 81.7	β = 90
c = 166.3	γ = 90

Software Package:

Software Name	Purpose
R-AXIS	data collection
R-AXIS	data reduction
X-PLOR	refinement
R-AXIS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-03-15 
• Released Date: 1996-08-01 
Deposition Author(s): Sheriff, S., Bajorath, J.

Revision History  

• Version 1.0: 1996-08-01
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary