4MSL Signaling Protein date Sep 18, 2013
title Crystal Structure Of The Vps10p Domain Of Human Sortilinnts Complex With Af40431
authors J.L.Andersen, D.Strandbygaard, S.Thirup
compound source
Molecule: Sortilin
Chain: A
Fragment: Vps10p Domain (Unp Residues 78-756)
Synonym: 100 Kda Nt Receptor, Glycoprotein 95, Gp95, Neurot Receptor 3, Nt3, Ntr3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sort1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell: Human Embryonic Kidney 293f Cells
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcep-Pu
symmetry Space Group: C 1 2 1
R_factor 0.205 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
160.876 79.165 111.700 90.00 127.27 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 2ET, BMA, MAN, NAG, PG4 enzyme
Primary referenceIdentification of the first small-molecule ligand of the neuronal receptor sortilin and structure determination of the receptor-ligand complex., Andersen JL, Schroder TJ, Christensen S, Strandbygard D, Pallesen LT, Garcia-Alai MM, Lindberg S, Langgard M, Eskildsen JC, David L, Tagmose L, Simonsen KB, Maltas PJ, Ronn LC, de Jong IE, Malik IJ, Egebjerg J, Karlsson JJ, Uppalanchi S, Sakumudi DR, Eradi P, Watson SP, Thirup S, Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):451-60. doi:, 10.1107/S1399004713030149. Epub 2014 Jan 29. PMID:24531479
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (233 Kb) [Save to disk]
  • Biological Unit Coordinates (4msl.pdb1.gz) 227 Kb
  • LPC: Ligand-Protein Contacts for 4MSL
  • CSU: Contacts of Structural Units for 4MSL
  • Structure Factors (550 Kb)
  • Retrieve 4MSL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4MSL from S2C, [Save to disk]
  • Re-refined 4msl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4MSL 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 4MSL
  • 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 4MSL, from MSDmotif at EBI
  • Fold representative 4msl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4msl_A] [4msl]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4MSL: [VPS10 ] by SMART
  • Other resources with information on 4MSL
  • Community annotation for 4MSL at PDBWiki (http://pdbwiki.org)

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