2EC8 Transferase date Feb 11, 2007
title Crystal Structure Of The Exctracellular Domain Of The Recept Tyrosine Kinase, Kit
authors S.Yuzawa, Y.Opatowsky, Z.Zhang, V.Mandiyan, I.Lax, J.Schlessinger
compound source
Molecule: Maststem Cell Growth Factor Receptor
Chain: A
Fragment: Extracellular Domains, D1-D5
Synonym: Scfr, Proto-Oncogene Tyrosine-Protein Kinase Kit, Cd117 Antigen;
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Kit
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfastbac1
symmetry Space Group: H 3
R_factor 0.254 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
162.249 162.249 67.586 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand NAG enzyme Transferase E.C.2.7.10.1 BRENDA
Primary referenceStructural Basis for Activation of the Receptor Tyrosine Kinase KIT by Stem Cell Factor., Yuzawa S, Opatowsky Y, Zhang Z, Mandiyan V, Lax I, Schlessinger J, Cell. 2007 Jul 27;130(2):323-34. PMID:17662946
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (2ec8.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 2EC8
  • CSU: Contacts of Structural Units for 2EC8
  • Structure Factors (212 Kb)
  • Retrieve 2EC8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2EC8 from S2C, [Save to disk]
  • Re-refined 2ec8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2EC8 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 2EC8
  • 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 2EC8, from MSDmotif at EBI
  • Fold representative 2ec8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ec8_A] [2ec8]
  • SWISS-PROT database: [P10721]
  • Domain organization of [KIT_HUMAN] by SWISSPFAM
  • Domains found in 2EC8: [IG] [IG_like] [IGc2 ] by SMART
  • Alignments of the sequence of 2EC8 with the sequences similar proteins can be viewed for 2EC8's classification [KIT_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [KIT_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2EC8
  • Community annotation for 2EC8 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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