2VIF Signaling Protein date Nov 30, 2007
title Crystal Structure Of Socs6 Sh2 Domain In Complex With A C-Ki Phosphopeptide
authors A.Bullock, A.C.W.Pike, P.Savitsky, T.Keates, E.S.Pilka, F.Von Del A.Edwards, J.Weigelt, C.H.Arrowsmith, S.Knapp
compound source
Molecule: Suppressor Of Cytokine Signalling 6
Chain: A
Fragment: Sh2 Domain, Residues 361-499
Synonym: Socs-6, Suppressor Of Cytokine Signaling 4, Socs-4 Cytokine-Inducible Sh2 Protein 4, Cis-4;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21-Elongin
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4

Molecule: Maststem Cell Growth Factor Receptor
Chain: P
Fragment: Residues 564-574
Synonym: Scfr, Proto-Oncogene Tyrosine-Protein Kinase Kit, Cd117 Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21-Elongin
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
symmetry Space Group: P 21 21 21
R_factor 0.139 R_Free 0.198
crystal
cell
length a length b length c angle alpha angle beta angle gamma
30.377 60.143 71.367 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand EDO, PTR enzyme
note 2VIF is a representative structure
Primary referenceStructural basis for c-KIT inhibition by the suppressor of cytokine signaling 6 (SOCS6) ubiquitin ligase., Zadjali F, Pike AC, Vesterlund M, Sun J, Wu C, Li SS, Ronnstrand L, Knapp S, Bullock AN, Flores-Morales A, J Biol Chem. 2010 Oct 28. PMID:21030588
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (2vif.pdb1.gz) 54 Kb
  • LPC: Ligand-Protein Contacts for 2VIF
  • CSU: Contacts of Structural Units for 2VIF
  • Likely Quarternary Molecular Structure file(s) for 2VIF
  • Structure Factors (305 Kb)
  • Retrieve 2VIF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VIF from S2C, [Save to disk]
  • Re-refined 2vif structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VIF 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 2VIF
  • 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 2VIF, from MSDmotif at EBI
  • Fold representative 2vif from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vif_A] [2vif] [2vif_P]
  • SWISS-PROT database: [P10721] [O14544]
  • Domain organization of [KIT_HUMAN] [SOCS6_HUMAN] by SWISSPFAM
  • Domain found in 2VIF: [SH2 ] by SMART
  • Alignments of the sequence of 2VIF with the sequences similar proteins can be viewed for 2VIF's classification [KIT_HUMAN] [SOCS6_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] [SOCS6_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2VIF
  • Community annotation for 2VIF 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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