4DEQ Protein Binding Cytokine date Jan 21, 2012
title Structure Of The Neuropilin-1vegf-A Complex
authors C.W.Vander Kooi
compound source
Molecule: Neuropilin-1, Vascular Endothelial Growth Factor
Chain: A, B
Fragment: Neuropilin B1 Domainvegf-A Heparin Binding Domai
Synonym: Vascular Endothelial Cell Growth Factor 165 Recept A, Vascular Permeability Factor, Vpf;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nrp1, Nrp, Vegf165r, Vegf, Vegfa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43
R_factor 0.209 R_Free 0.267
length a length b length c angle alpha angle beta angle gamma
114.978 114.978 50.946 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.65 Å
ligand PO4 enzyme
A, B

Primary referenceStructural basis for the selective vascular endothelial growth factor-A (VEGF-A) binding to neuropilin-1., Parker MW, Xu P, Li X, Vander Kooi CW, J Biol Chem. 2012 Feb 7. PMID:22318724
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (152 Kb) [Save to disk]
  • Biological Unit Coordinates (4deq.pdb1.gz) 147 Kb
  • Biological Unit Coordinates (4deq.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (4deq.pdb3.gz) 74 Kb
  • LPC: Ligand-Protein Contacts for 4DEQ
  • CSU: Contacts of Structural Units for 4DEQ
  • Structure Factors (272 Kb)
  • Retrieve 4DEQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DEQ from S2C, [Save to disk]
  • Re-refined 4deq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DEQ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4DEQ
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4DEQ, from MSDmotif at EBI
  • Fold representative 4deq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4deq_A] [4deq_B] [4deq]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DEQ: [FA58C ] by SMART
  • Other resources with information on 4DEQ
  • Community annotation for 4DEQ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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