4N7E Signaling Protein date Oct 15, 2013
title Crystal Structure Of The Vps10p Domain Of Human Sortilinnts Complex With Af38469
authors J.L.Andersen, D.Strandbygaard, S.Thirup
compound source
Molecule: Sortilin
Chain: A
Fragment: Unp Residues 78-756
Synonym: 100 Kda Nt Receptor, Glycoprotein 95, Gp95, Neurot Receptor 3, Nt3, Ntr3;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sort1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell: Hek 293f Cell
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcep-Pu
symmetry Space Group: C 1 2 1
R_factor 0.201 R_Free 0.242
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.948 77.402 111.176 90.00 127.06 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 2JQ, BMA, NAG, PGE enzyme
Primary referenceThe identification of AF38469: An orally bioavailable inhibitor of the VPS10P family sorting receptor Sortilin., Schroder TJ, Christensen S, Lindberg S, Langgard M, David L, Maltas PJ, Eskildsen J, Jacobsen J, Tagmose L, Simonsen KB, Biilmann Ronn LC, de Jong IE, Malik IJ, Karlsson JJ, Bundgaard C, Egebjerg J, Stavenhagen JB, Strandbygard D, Thirup S, Andersen JL, Uppalanchi S, Pervaram S, Kasturi SP, Eradi P, Sakumudi DR, Watson SP, Bioorg Med Chem Lett. 2014 Jan 1;24(1):177-80. doi: 10.1016/j.bmcl.2013.11.046., Epub 2013 Nov 27. PMID:24355129
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (232 Kb) [Save to disk]
  • Biological Unit Coordinates (4n7e.pdb1.gz) 226 Kb
  • LPC: Ligand-Protein Contacts for 4N7E
  • CSU: Contacts of Structural Units for 4N7E
  • Structure Factors (544 Kb)
  • Retrieve 4N7E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4N7E from S2C, [Save to disk]
  • Re-refined 4n7e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4N7E 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 4N7E
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4N7E, from MSDmotif at EBI
  • Fold representative 4n7e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4n7e_A] [4n7e]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4N7E: [VPS10 ] by SMART
  • Other resources with information on 4N7E
  • Community annotation for 4N7E at PDBWiki (http://pdbwiki.org)

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