3F6K Signaling Protein date Nov 06, 2008
title Crystal Structure Of The Vps10p Domain Of Human Sortilinnts Complex With Neurotensin
authors E.M.Quistgaard, P.Madsen, M.K.Groftehauge, P.Nissen, C.M.Peterse S.Thirup
compound source
Molecule: Sortilin
Chain: A
Fragment: Unp Residues 78-756
Synonym: Neurotensin Receptor 3, Ntr3, Nts3, Glycoprotein 9 100 Kda Nt Receptor;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Sort1
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_strain: Cho-K1

Molecule: Neurotensin
Chain: N
Fragment: Unp Residues 151-163
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Peptide Purchased From Sigma. It R The Naturally Occurring Form Of Neurotensin In Human, Resid 163 Of Uniprot Entry P30990, Neut_human
symmetry Space Group: C 1 2 1
R_factor 0.204 R_Free 0.229
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.760 74.530 108.330 90.00 131.87 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand BMA, GOL, NAG, PGE enzyme
Primary referenceLigands bind to Sortilin in the tunnel of a ten-bladed beta-propeller domain., Quistgaard EM, Madsen P, Groftehauge MK, Nissen P, Petersen CM, Thirup SS, Nat Struct Mol Biol. 2009 Jan;16(1):96-8. Epub 2009 Jan 4. PMID:19122660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (3f6k.pdb1.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 3F6K
  • CSU: Contacts of Structural Units for 3F6K
  • Likely Quarternary Molecular Structure file(s) for 3F6K
  • Structure Factors (525 Kb)
  • Retrieve 3F6K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F6K from S2C, [Save to disk]
  • Re-refined 3f6k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F6K 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 3F6K
  • 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 3F6K, from MSDmotif at EBI
  • Fold representative 3f6k from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f6k] [3f6k_A] [3f6k_N]
  • SWISS-PROT database: [P30990] [Q99523]
  • Belongs to the retromer-dependent vacuolar protein sorting (r-vps) family according to TCDB.
  • Domain organization of [NEUT_HUMAN] [SORT_HUMAN] by SWISSPFAM
  • Domain found in 3F6K: [VPS10 ] by SMART
  • Other resources with information on 3F6K
  • Community annotation for 3F6K 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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