2CI9 Protein Binding date Mar 17, 2006
title Nck1 Sh2-Domain In Complex With A Dodecaphosphopeptide From Protein Tir
authors S.Frese, W.D.Schubert, A.C.Findeis, T.Marquardt, Y.S.Roske, T.E.B.Stradal, D.W.Heinz
compound source
Molecule: Cytoplasmic Protein Nck1
Chain: A, B
Fragment: Sh2-Domain, Residues 281-377
Synonym: Nck Adaptor Protein 1, Sh2sh3 Adaptor Protein Nck
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pgex-6p-1 (Amersham Biosciences)

Molecule: Translocated Intimin Receptor
Chain: L, M
Fragment: Phosphopeptide Ligand Of Nck-Sh2, Residues 469-48
Engineered: Yes
Other_details: The Peptide Was Synthesized Chemically

Synthetic: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.196 R_Free 0.235
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.092 60.518 65.061 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.50 Å
ligand PTR enzyme
Primary referenceThe phosphotyrosine peptide binding specificity of Nck1 and Nck2 Src homology 2 domains., Frese S, Schubert WD, Findeis AC, Marquardt T, Roske YS, Stradal TE, Heinz DW, J Biol Chem. 2006 Jun 30;281(26):18236-45. Epub 2006 Apr 24. PMID:16636066
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (2ci9.pdb1.gz) 23 Kb
  • Biological Unit Coordinates (2ci9.pdb2.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 2CI9
  • CSU: Contacts of Structural Units for 2CI9
  • Likely Quarternary Molecular Structure file(s) for 2CI9
  • Structure Factors (254 Kb)
  • Retrieve 2CI9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2CI9 from S2C, [Save to disk]
  • Re-refined 2ci9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2CI9 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 2CI9
  • 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 2CI9, from MSDmotif at EBI
  • Fold representative 2ci9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ci9_B] [2ci9_A] [2ci9_L] [2ci9] [2ci9_M]
  • SWISS-PROT database: [P16333] [O50190]
  • Domain organization of [NCK1_HUMAN] [O50190_ECOLX] by SWISSPFAM
  • Domain found in 2CI9: [SH2 ] by SMART
  • Other resources with information on 2CI9
  • Community annotation for 2CI9 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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