3S35

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 stru ...

    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: 2
MoleculeChainsSequence LengthOrganismDetails
6.64 Fab light chainL217Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 2X122Homo sapiensMutation(s): 0 
Gene Names: KDRFLK1VEGFR2
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
NIH Common Fund Data Resources
PHAROS  P35968
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6.64 Fab heavy chainH217Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
A
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
X
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
H, L, X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.937α = 90
b = 112.13β = 90
c = 156.971γ = 90
Software Package:
Software NamePurpose
APSdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary