3O5X Hydrolase date Jul 28, 2010
title Crystal Structure Of The Oncogenic Tyrosine Phosphatase Shp2 With A Salicylic Acid-Based Small Molecule Inhibitor
authors Z.Y.Zhang, X.Zhang, Y.He, S.Liu, Z.Yu, Z.Jiang, Z.Yang, Y.Dong, S.C.Nabinger, L.Wu, A.M.Gunawan, L.Wang, R.J.Chan
compound source
Molecule: Tyrosine-Protein Phosphatase Non-Receptor Type 11
Chain: A
Fragment: Unp Residues 262-532, Catalytic Domain
Synonym: Protein-Tyrosine Phosphatase 2c, Ptp-2c, Protein-T Phosphatase 1d, Ptp-1d, Sh-Ptp3, Sh-Ptp2, Shp-2, Shp2;
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.238
length a length b length c angle alpha angle beta angle gamma
39.544 75.829 48.214 90.00 98.53 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand JZG BindingDB enzyme Hydrolase E.C. BRENDA
note 3O5X supersedes 3JRL
Primary referenceSalicylic Acid Based Small Molecule Inhibitor for the Oncogenic Src Homology-2 Domain Containing Protein Tyrosine Phosphatase-2 (SHP2)., Zhang X, He Y, Liu S, Yu Z, Jiang ZX, Yang Z, Dong Y, Nabinger SC, Wu L, Gunawan AM, Wang L, Chan RJ, Zhang ZY, J Med Chem. 2010 Feb 19. PMID:20170098
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (50 Kb) [Save to disk]
  • Biological Unit Coordinates (3o5x.pdb1.gz) 46 Kb
  • LPC: Ligand-Protein Contacts for 3O5X
  • CSU: Contacts of Structural Units for 3O5X
  • Structure Factors (363 Kb)
  • Retrieve 3O5X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3O5X from S2C, [Save to disk]
  • Re-refined 3o5x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3O5X 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 3O5X
  • 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 3O5X, from MSDmotif at EBI
  • Fold representative 3o5x from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3o5x_A] [3o5x]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3O5X: [PTPc ] by SMART
  • Alignments of the sequence of 3O5X with the sequences similar proteins can be viewed for 3O5X'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 3O5X
  • Community annotation for 3O5X 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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