5KMO Transferase Transferase Inhibitor date Jun 27, 2016
title Trka Jm-Kinase With 1-(2-Methyl-4-Phenyl-Pyrimidin-5-Yl)-3-( Pyridyl)Urea
authors H.P.Su
compound source
Molecule: High Affinity Nerve Growth Factor Receptor
Chain: A
Fragment: Catalytic Domain With Juxtamembrane Region, Unp R 376-698;
Synonym: Neurotrophic Tyrosine Kinase Receptor Type 1,Trk1- Transforming Tyrosine Kinase Protein,Tropomyosin-Related Ki Tyrosine Kinase Receptor,Tyrosine Kinase Receptor A,Trk-A,G P140-Trka;
Ec: 2.7.10.1
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ntrk1, Mtc, Trk, Trka
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
symmetry Space Group: P 31 1 2
R_factor 0.194 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.810 51.810 229.550 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.67 Å
ligand 6UM enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural characterization of nonactive site, TrkA-selective kinase inhibitors., Su HP, Rickert K, Burlein C, Narayan K, Bukhtiyarova M, Hurzy DM, Stump CA, Zhang X, Reid J, Krasowska-Zoladek A, Tummala S, Shipman JM, Kornienko M, Lemaire PA, Krosky D, Heller A, Achab A, Chamberlin C, Saradjian P, Sauvagnat B, Yang X, Ziebell MR, Nickbarg E, Sanders JM, Bilodeau MT, Carroll SS, Lumb KJ, Soisson SM, Henze DA, Cooke AJ, Proc Natl Acad Sci U S A. 2016 Dec 30. pii: 201611577. doi:, 10.1073/pnas.1611577114. PMID:28039433
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (5kmo.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 5KMO
  • CSU: Contacts of Structural Units for 5KMO
  • Structure Factors (699 Kb)
  • Retrieve 5KMO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5KMO from S2C, [Save to disk]
  • Re-refined 5kmo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5KMO 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 5KMO
  • 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: [5kmo] [5kmo_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5KMO
  • Community annotation for 5KMO at PDBWiki (http://pdbwiki.org)

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