4QDQ Cell Adhesion date May 14, 2014
title Physical Basis For Nrp2 Ligand Binding
authors M.W.Parker, C.W.Vander Kooi
compound source
Molecule: Neuropilin-2
Chain: A, B
Fragment: Neuropilin-2 B1b2 Domain, Vegf-C C-Terminus
Synonym: Vascular Endothelial Cell Growth Factor 165 Recept
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nrp2, Vegf165r2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta-Gami 2(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 1 21 1
R_factor 0.210 R_Free 0.241
length a length b length c angle alpha angle beta angle gamma
41.047 120.808 69.837 90.00 103.29 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand GOL, SO4 enzyme
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] (227 Kb) [Save to disk]
  • Biological Unit Coordinates (4qdq.pdb1.gz) 223 Kb
  • Biological Unit Coordinates (4qdq.pdb2.gz) 223 Kb
  • LPC: Ligand-Protein Contacts for 4QDQ
  • CSU: Contacts of Structural Units for 4QDQ
  • Structure Factors (883 Kb)
  • Retrieve 4QDQ in mmCIF format [Save to disk]
  • Re-refined 4qdq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4QDQ 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 4QDQ
  • 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 4QDQ, from MSDmotif at EBI
  • Fold representative 4qdq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4qdq_A] [4qdq] [4qdq_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4QDQ: [FA58C ] by SMART
  • Other resources with information on 4QDQ
  • Community annotation for 4QDQ at PDBWiki (http://pdbwiki.org)

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