1KMX

Heparin-binding Domain from Vascular Endothelial Growth Factor

• PDB DOI: https://doi.org/10.2210/pdb1KMX/pdb
• BMRB: 5238

• Classification: HORMONE/GROWTH FACTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-17 Released: 2002-07-24 
• Deposition Author(s): Stauffer, M.E., Skelton, N.J., Fairbrother, W.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

Refinement of the Solution Structure of the Heparin-binding Domain of Vascular Endothelial Growth Factor using Residual Dipolar Couplings

Stauffer, M.E., Skelton, N.J., Fairbrother, W.J.

(2002) J Biomol NMR 23: 57-61

• PubMed: 12061718 
• DOI: https://doi.org/10.1023/a:1015346504499
• Primary Citation of Related Structures:  
  1KMX


• PubMed Abstract: 
  

  Previous NMR structural studies of the heparin-binding domain of vascular endothelial growth factor (VEGF165) revealed a novel fold comprising two subdomains, each containing two disulfide bridges and a short two-stranded antiparallel beta-sheet. The mutual orientation of the two subdomains was poorly defined by the NMR data. Heteronuclear relaxation data suggested that this disorder resulted from a relative lack of experimental restraints due to the limited size of the interface, rather than inherent high-frequency flexibility. Refinement of the structure using 1H(N-15N residual dipolar coupling restraints results in significantly improved definition of the relative subdomain orientations.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.5 kDa 
• Atom Count: 444 
• Modelled Residue Count: 55 
• Deposited Residue Count: 55 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
vascular endothelial growth factor	A	55	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
PHAROS:  P15692 GTEx:  ENSG00000112715

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-24 
Deposition Author(s): Stauffer, M.E., Skelton, N.J., Fairbrother, W.J.

Revision History  

• Version 1.0: 2002-07-24
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-09
  Changes: Data collection, Structure summary