5MYA Signaling Protein date Jan 26, 2017
title Homodimerization Of Tie2 Fibronectin-Like Domains 1-3 In Spa C2
authors V.M.Leppanen, P.Saharinen, K.Alitalo
compound source
Molecule: Angiopoietin-1 Receptor
Chain: A, B
Synonym: Endothelial Tyrosine Kinase,Tunica Interna Endothe Kinase,Tyrosine Kinase With Ig And Egf Homology Domains-2,T Protein Kinase Receptor Tek,Tyrosine-Protein Kinase Recepto Htie2,P140 Tek;
Ec: 2.7.10.1
Engineered: Yes
Other_details: In Addition To The Tie2 Fn-Like Domains, The Includes Mellitin Signal Peptide, A N-Terminal Cloning Arte (Adp), C-Terminal Factor Xa Cleavage Site (Iegr) And His-Ta First Fn-Like Domain In Chain B Was Disordered Due To Lack Packing Contacts And Was Omitted From Model Building.
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tek, Tie2, Vmcm, Vmcm1
Expression_system: Spodoptera Aff. Frugiperda 2 Rz-2014
Expression_system_taxid: 1491790
symmetry Space Group: C 1 2 1
R_factor 0.235 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
134.160 104.690 79.520 90.00 121.41 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand BMA, MAN, NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceStructural basis of Tie2 activation and Tie2/Tie1 heterodimerization., Leppanen VM, Saharinen P, Alitalo K, Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4376-4381. doi:, 10.1073/pnas.1616166114. Epub 2017 Apr 10. PMID:28396439
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (174 Kb) [Save to disk]
  • Biological Unit Coordinates (5mya.pdb1.gz) 165 Kb
  • LPC: Ligand-Protein Contacts for 5MYA
  • CSU: Contacts of Structural Units for 5MYA
  • Structure Factors (199 Kb)
  • Retrieve 5MYA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MYA from S2C, [Save to disk]
  • Re-refined 5mya structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5MYA 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 5MYA
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5mya] [5mya_A] [5mya_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MYA
  • Community annotation for 5MYA at PDBWiki (http://pdbwiki.org)

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