3QTK

The crystal structure of chemically synthesized VEGF-A

• PDB DOI: https://doi.org/10.2210/pdb3QTK/pdb

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


• Deposited: 2011-02-22 Released: 2011-07-27 
• Deposition Author(s): Mandal, K., Kent, S.B.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.223 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Total chemical synthesis of biologically active vascular endothelial growth factor.

Mandal, K., Kent, S.B.

(2011) Angew Chem Int Ed Engl 50: 8029-8033

• PubMed: 21744452 
• DOI: https://doi.org/10.1002/anie.201103237
• Primary Citation of Related Structures:  
  3QTK


• PubMed Abstract: 
  

  Efficient access: the 204-residue covalent-dimer vascular endothelial growth factor with full mitogenic activity was prepared from three unprotected peptide segments by one-pot native chemical ligations. The covalent structure of the synthetic VEGF was confirmed by precise mass measurement, and the three-dimensional structure of the synthetic protein was determined by high-resolution X-ray crystallography.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.22 kDa 
• Atom Count: 5,274 
• Modelled Residue Count: 576 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A, B [auth D], C [auth B], D [auth C], E, F	102	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Go to UniProtKB:  P15692
PHAROS:  P15692 GTEx:  ENSG00000112715

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TFA	H [auth A], J [auth A], K [auth A], M [auth D], O [auth B], X [auth F]	trifluoroacetic acid C2 H F3 O2 DTQVDTLACAAQTR-UHFFFAOYSA-N
GOL	I [auth A], N [auth D], R [auth C], S [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A], L [auth D], P [auth B], Q [auth C], T [auth C], U [auth E], V [auth E], W [auth F]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.223 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 230.922	α = 90
b = 44.008	β = 99.93
c = 73.111	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-27 
Deposition Author(s): Mandal, K., Kent, S.B.H.

Revision History  

• Version 1.0: 2011-07-27
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary