1BJ1

VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY

• PDB DOI:  https://doi.org/10.2210/pdb1BJ1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-30 Released: 1999-01-13 
• Deposition Author(s): Muller, Y.A., Christinger, H.W., De Vos, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface.

Muller, Y.A., Chen, Y., Christinger, H.W., Li, B., Cunningham, B.C., Lowman, H.B., de Vos, A.M.

(1998) Structure 6: 1153-1167

• PubMed: 9753694 
• DOI: https://doi.org/10.1016/s0969-2126(98)00116-6
• Primary Citation of Related Structures:  
  1BJ1


• PubMed Abstract: 
  

Vascular endothelial growth factor (VEGF) is a highly specific angiogenic growth factor; anti-angiogenic treatment through inhibition of receptor activation by VEGF might have important therapeutic applications in diseases such as diabetic retinopathy and cancer. A neutralizing anti-VEGF antibody shown to suppress tumor growth in an in vivo murine model has been used as the basis for production of a humanized version.

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Related Citations: 

• Antibody Humanization Using Monovalent Phage Display
  Baca, M., Presta, L.G., O'Connor, S.J., Wells, J.A.
  (1997) J Biol Chem 272: 10678

• Humanization of an Anti-Vascular Endothelial Growth Factor Monoclonal Antibody for the Therapy of Solid Tumors and Other Disorders
  Presta, L.G., Chen, H., O'Connor, S.J., Chisholm, V., Meng, Y.G., Krummen, L., Winkler, M., Ferrara, N.
  (1997) Cancer Res 57: 4593

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Organizational Affiliation: 

Department of Protein Engineering Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 120.81 kDa 
• Atom Count: 8,694 
• Modelled Residue Count: 1,050 
• Deposited Residue Count: 1,094 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment, light chain	A [auth L], E [auth J]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment, heavy chain	B [auth H], F [auth K]	231	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	C [auth V], D [auth W]	102	Homo sapiens	Mutation(s): 0  Gene Names: VEGFA, VEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
PHAROS:  P15692

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth H], H [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.266 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.86	α = 90
b = 66.98	β = 94.27
c = 140.51	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Muller, Y.A., Christinger, H.W., De Vos, A.M.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-09-26
  Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.4: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description