1PKG Transferase Activator date Jun 05, 2003
title Structure Of A C-Kit Kinase Product Complex
authors C.D.Mol, K.B.Lim, V.Sridhar, H.Zou, E.Y.T.Chien, B.C.Sang, J.Nowa D.B.Kassel, C.N.Cronin, D.E.Mcree
compound source
Molecule: C-Kit Protein
Chain: A, B
Fragment: Catalytic Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_vector: Psxb1 (Modified Version Of Pfastb (Invitrogen))
symmetry Space Group: P 21 21 2
R_factor 0.225 R_Free 0.311
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.667 116.458 60.066 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand ADP, MG, PTR enzyme
related structures by homologous chain: 1T45
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of a c-kit product complex reveals the basis for kinase transactivation., Mol CD, Lim KB, Sridhar V, Zou H, Chien EY, Sang BC, Nowakowski J, Kassel DB, Cronin CN, McRee DE, J Biol Chem 2003 Aug 22;278(34):31461-4. Epub 2003 Jun 24. PMID:12824176
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (100 Kb) [Save to disk]
  • Biological Unit Coordinates (1pkg.pdb1.gz) 48 Kb
  • Biological Unit Coordinates (1pkg.pdb2.gz) 47 Kb
  • Biological Unit Coordinates (1pkg.pdb3.gz) 182 Kb
  • LPC: Ligand-Protein Contacts for 1PKG
  • CSU: Contacts of Structural Units for 1PKG
  • Likely Quarternary Molecular Structure file(s) for 1PKG
  • Retrieve 1PKG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PKG from S2C, [Save to disk]
  • View 1PKG 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 1PKG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1PKG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pkga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pkgb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1pkg from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1pkg_B] [1pkg] [1pkg_A]
  • SWISS-PROT database: [P10721]
  • Domain organization of [KIT_HUMAN] by SWISSPFAM
  • Domain found in 1PKG: [TyrKc ] by SMART
  • Alignments of the sequence of 1PKG with the sequences similar proteins can be viewed for 1PKG'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 1PKG
  • Community annotation for 1PKG 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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