3I97 Signaling Protein date Jul 10, 2009
title B1 Domain Of Human Neuropilin-1 Bound With Small Molecule Eg
authors C.K.Allerston, S.Djordjevic
compound source
Molecule: Neuropilin-1
Chain: A, B
Fragment: Domain B1, F58 Type C 1
Synonym: Vascular Endothelial Cell Growth Factor 165 Recept
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Np1-B1, Nrp, Nrp1, Vegf165r
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
symmetry Space Group: P 1 21 1
R_factor 0.216 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
41.000 89.600 41.600 90.00 97.70 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 8DR, GOL BindingDB enzyme
Primary referenceSmall Molecule Inhibitors of the Neuropilin-1 Vascular Endothelial Growth Factor A (VEGF-A) Interaction., Jarvis A, Allerston CK, Jia H, Herzog B, Garza-Garcia A, Winfield N, Ellard K, Aqil R, Lynch R, Chapman C, Hartzoulakis B, Nally J, Stewart M, Cheng L, Menon M, Tickner M, Djordjevic S, Driscoll PC, Zachary I, Selwood DL, J Med Chem. 2010 Feb 12. PMID:20151671
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (3i97.pdb1.gz) 26 Kb
  • Biological Unit Coordinates (3i97.pdb2.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 3I97
  • CSU: Contacts of Structural Units for 3I97
  • Structure Factors (95 Kb)
  • Retrieve 3I97 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I97 from S2C, [Save to disk]
  • Re-refined 3i97 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3I97 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 3I97
  • 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 3I97, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i97] [3i97_B] [3i97_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3I97: [FA58C ] by SMART
    • Other resources with information on 3I97
  • Community annotation for 3I97 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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