2NV5

Crystal structure of a C-terminal phosphatase domain of Rattus norvegicus ortholog of human protein tyrosine phosphatase, receptor type, D (PTPRD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Structural genomics of protein phosphatases.

Almo, S.C.Bonanno, J.B.Sauder, J.M.Emtage, S.Dilorenzo, T.P.Malashkevich, V.Wasserman, S.R.Swaminathan, S.Eswaramoorthy, S.Agarwal, R.Kumaran, D.Madegowda, M.Ragumani, S.Patskovsky, Y.Alvarado, J.Ramagopal, U.A.Faber-Barata, J.Chance, M.R.Sali, A.Fiser, A.Zhang, Z.Y.Lawrence, D.S.Burley, S.K.

(2007) J.STRUCT.FUNCT.GENOM. 8: 121-140

  • DOI: 10.1007/s10969-007-9036-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phos ...

    The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.


    Organizational Affiliation

    Albert Einstein College of Medicine, Bronx, NY, USA. almo@aecom.yu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PTPRD, PHOSPHATASE
A, B, C
299Rattus norvegicusMutation(s): 0 
Gene Names: Ptprs
EC: 3.1.3.48
Find proteins for Q64605 (Rattus norvegicus)
Go to UniProtKB:  Q64605
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 140.789α = 90.00
b = 140.789β = 90.00
c = 112.431γ = 120.00
Software Package:
Software NamePurpose
SHELXDphasing
CCP4data scaling
REFMACrefinement
MAR345data collection
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-03-20
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-10-24
    Type: Structure summary
  • Version 1.4: 2017-10-18
    Type: Refinement description
  • Version 1.5: 2018-11-14
    Type: Data collection, Structure summary