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;
Ec: 3.1.3.48
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
crystal
cell
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.3.1.3.48 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
  • Alignments of the sequence of 3TKZ with the sequences similar proteins can be viewed for 3TKZ's classification 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 at ProtoMap. Click on the Cluster number.
  • 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.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science