4QDS Physical basis for Nrp2 ligand binding date
authors Parker, M.W., Kooi, C.W.Vander.
compound source
symmetry
R_factor
R_Free 0.26388
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand ACT, GOL enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Basis for VEGF-C Binding to Neuropilin-2 and Sequestration by a Soluble Splice Form., Parker MW, Linkugel AD, Goel HL, Wu T, Mercurio AM, Vander Kooi CW, Structure. 2015 Apr 7;23(4):677-87. doi: 10.1016/j.str.2015.01.018. Epub 2015 Mar, 5. PMID:25752543
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (4qds.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 4QDS
  • CSU: Contacts of Structural Units for 4QDS
  • Structure Factors (320 Kb)
  • Retrieve 4QDS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4QDS from S2C, [Save to disk]
  • Re-refined 4qds structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4QDS 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 4QDS
  • 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
  • 3D motif for 4QDS, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qds_B] [4qds] [4qds_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4QDS: [FA58C ] by SMART
    • Other resources with information on 4QDS
  • Community annotation for 4QDS at PDBWiki (http://pdbwiki.org)

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