2E9W Transferase Hormone date Jan 27, 2007
title Crystal Structure Of The Extracellular Domain Of Kit In Comp Stem Cell Factor (Scf)
authors S.Yuzawa, Y.Opatowsky, Z.Zhang, V.Mandiyan, I.Lax, J.Schlessinger
compound source
Molecule: Maststem Cell Growth Factor Receptor
Chain: A, B
Fragment: Extracellular Domains, D1 - D5
Synonym: Scfr, Proto-Oncogene Tyrosine-Protein Kinase Kit, Cd117 Antigen;
Engineered: Yes
Mutation: 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: Pbluebac III

Molecule: Kit Ligand
Chain: C, D
Fragment: Soluble Form, Residues 26 - 166
Synonym: C-Kit Ligand, Stem Cell Factor, Scf, Mast Cell Gro Factor, Mgf;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Scf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Mgt7
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: C 1 2 1
R_factor 0.245 R_Free 0.294
length a length b length c angle alpha angle beta angle gamma
269.477 52.072 189.791 90.00 108.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand NAG enzyme Transferase E.C. BRENDA
D, C

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] (193 Kb) [Save to disk]
  • Biological Unit Coordinates (2e9w.pdb1.gz) 186 Kb
  • LPC: Ligand-Protein Contacts for 2E9W
  • CSU: Contacts of Structural Units for 2E9W
  • Structure Factors (278 Kb)
  • Retrieve 2E9W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2E9W from S2C, [Save to disk]
  • Re-refined 2e9w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2E9W 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 2E9W
  • 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 2E9W, from MSDmotif at EBI
  • Fold representative 2e9w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2e9w_A] [2e9w_C] [2e9w_D] [2e9w] [2e9w_B]
  • SWISS-PROT database: [P10721] [P21583]
  • Domain organization of [KIT_HUMAN] [SCF_HUMAN] by SWISSPFAM
  • Domains found in 2E9W: [IG_like] [IGc2 ] by SMART
  • Other resources with information on 2E9W
  • Community annotation for 2E9W 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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