3TKZ Hydrolase Peptide date Aug 29, 2011
title Structure Of The Shp-2 N-Sh2 Domain In A 1:2 Complex With Rv Peptide
authors Y.Zhang, J.Zhang, C.Yuan, R.L.Hard, I.H.Park, C.Li, C.E.Bell, D.Pei
compound source
Molecule: Tyrosine-Protein Phosphatase Non-Receptor Type 11
Chain: A
Fragment: N-Terminal Sh2 Domain (Unp Residues 1-106)
Synonym: Protein-Tyrosine Phosphatase 1d, Ptp-1d, Protein-T Phosphatase 2c, Ptp-2c, Sh-Ptp2, Shp-2, Shp2, Sh-Ptp3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptpn11, Ptp2c, Shptp2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Protein (Rvipyfvplnr Peptide)
Chain: P, Q
Engineered: Yes
Other_details: Y4 Residue Is Phosphorylated

Synthetic: Yes
Other_details: The Peptide Was Synthesized Using Standard F Chemistry
symmetry Space Group: P 43 21 2
R_factor 0.197 R_Free 0.216
length a length b length c angle alpha angle beta angle gamma
62.865 62.865 75.322 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand PTR enzyme Hydrolase E.C. BRENDA
Primary referenceSimultaneous binding of two peptidyl ligands by a SRC homology 2 domain., Zhang Y, Zhang J, Yuan C, Hard RL, Park IH, Li C, Bell C, Pei D, Biochemistry. 2011 Sep 6;50(35):7637-46. Epub 2011 Aug 9. PMID:21800896
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (3tkz.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3TKZ
  • CSU: Contacts of Structural Units for 3TKZ
  • Structure Factors (95 Kb)
  • Retrieve 3TKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TKZ from S2C, [Save to disk]
  • Re-refined 3tkz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3TKZ 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 3TKZ
  • 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 3TKZ, from MSDmotif at EBI
  • Fold representative 3tkz from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tkz_A] [3tkz_Q] [3tkz_P] [3tkz]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3TKZ: [SH2 ] by SMART
  • Other resources with information on 3TKZ
  • Community annotation for 3TKZ at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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