3S34

Structure of the 1121B Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies.

Franklin, M.C.Navarro, E.C.Wang, Y.Patel, S.Singh, P.Zhang, Y.Persaud, K.Bari, A.Griffith, H.Shen, L.Balderes, P.Kussie, P.

(2011) Structure 19: 1097-1107

  • DOI: https://doi.org/10.1016/j.str.2011.01.019
  • Primary Citation of Related Structures:  
    3S34, 3S35, 3S36, 3S37

  • PubMed Abstract: 

    The anti-VEGF receptor 2 antibody IMC-1121B is a promising antiangiogenic drug being tested for treatment of breast and gastric cancer. We have determined the structure of the 1121B Fab fragment in complex with domain 3 of VEGFR2, as well as the structure of a different neutralizing anti-VEGFR2 antibody, 6.64, also in complex with VEGFR2 domain 3. The two Fab fragments bind at opposite ends of VEGFR2 domain 3; 1121B directly blocks VEGF binding, whereas 6.64 may prevent receptor dimerization by perturbing the domain 3:domain 4 interface. Mutagenesis reveals that residues essential for VEGF, 1121B, and 6.64 binding are nonoverlapping among the three contact patches.


  • Organizational Affiliation

    Department of Immunology, ImClone Systems, New York, NY 10014, USA. mfranklin@nysbc.org


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1121B Fab light chainA [auth L]214Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
1121B Fab heavy chainB [auth H]221Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth H]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.426α = 90
b = 66.426β = 90
c = 203.868γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Advisory, Source and taxonomy
  • Version 1.2: 2023-09-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description