3S36

Structural basis for the function of two anti-VEGF receptor antibodies


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
1121B light chainA [auth L]214Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
1121B heavy chainB [auth H]221Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2C [auth X]122Homo sapiensMutation(s): 0 
Gene Names: FLK1KDRVEGFR2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.277 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.864α = 90
b = 64.864β = 90
c = 263.161γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-05-17 
  • Released Date: 2011-08-24 
  • Deposition Author(s): Franklin, M.C.

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Source and taxonomy