2V5Y Hydrolase date Jul 11, 2007
title Crystal Structure Of The Receptor Protein Tyrosine Phosphata Ectodomain
authors A.R.Aricescu, C.Siebold, K.Choudhuri, V.T.Chang, W.Lu, S.J.Davis, Der Merwe, E.Y.Jones
compound source
Molecule: Receptor-Type Tyrosine-Protein Phosphatase Mu
Chain: A
Fragment: Extracellular Region, Residues 21-742
Synonym: Protein-Tyrosine Phosphatase Mu, R-Ptp-Mu
Ec: 3.1.3.48
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Lung
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek-293s Gnti-
Expression_system_vector_type: Episomal Plasmid
Expression_system_plasmid: Phlsec
symmetry Space Group: C 1 2 1
R_factor 0.242 R_Free 0.320
crystal
cell
length a length b length c angle alpha angle beta angle gamma
167.336 69.325 97.487 90.00 113.52 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand NA, NAG enzyme Hydrolase E.C.3.1.3.48 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism., Aricescu AR, Siebold C, Choudhuri K, Chang VT, Lu W, Davis SJ, van der Merwe PA, Jones EY, Science. 2007 Aug 31;317(5842):1217-20. PMID:17761881
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (98 Kb) [Save to disk]
  • Biological Unit Coordinates (2v5y.pdb1.gz) 177 Kb
  • LPC: Ligand-Protein Contacts for 2V5Y
  • CSU: Contacts of Structural Units for 2V5Y
  • Likely Quarternary Molecular Structure file(s) for 2V5Y
  • Structure Factors (165 Kb)
  • Retrieve 2V5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V5Y from S2C, [Save to disk]
  • Re-refined 2v5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V5Y 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 2V5Y
  • 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 2V5Y, from MSDmotif at EBI
  • Fold representative 2v5y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v5y] [2v5y_A]
  • SWISS-PROT database: [P28827]
  • Domain organization of [PTPRM_HUMAN] by SWISSPFAM
  • Domains found in 2V5Y: [FN3] [IG] [MAM ] by SMART
  • Other resources with information on 2V5Y
  • Community annotation for 2V5Y 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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