3NFL Protein Binding date Jun 10, 2010
title Crystal Structure Of The Ptpn4 Pdz Domain Complexed With The Terminus Of The Glun2a Nmda Receptor Subunit
authors N.Babault, F.Cordier, M.Lafage, J.Cockburn, A.Haouz, F.A.Rey, M.De H.Buc, M.Lafon, N.Wolff
compound source
Molecule: Tyrosine-Protein Phosphatase Non-Receptor Type 4
Chain: A, B, C, D
Fragment: Pdz Domain (Unp Residues 499-604)
Synonym: Protein-Tyrosine Phosphatase Meg1, Ptpase-Meg1, Me
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ptpn4
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3) Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdest15

Molecule: Glutamate [Nmda] Receptor Subunit Epsilon-1
Chain: E, F, G, H
Fragment: Unp Residues 1449-1464
Synonym: N-Methyl D-Aspartate Receptor Subtype 2a, Nmdar2a, Hnr2a;
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Other_details: Nr2a16 Peptide Has Been Chemically Synthetiz Sequence Ocuurs Naturally In Homo Sapiens (Human)
symmetry Space Group: P 21 21 21
R_factor 0.217 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.582 51.679 190.902 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.91 Å
Primary referencePeptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death., Babault N, Cordier F, Lafage M, Cockburn J, Haouz A, Prehaud C, Rey FA, Delepierre M, Buc H, Lafon M, Wolff N, Structure. 2011 Oct 12;19(10):1518-24. PMID:22000519
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (3nfl.pdb1.gz) 35 Kb
  • Biological Unit Coordinates (3nfl.pdb2.gz) 34 Kb
  • Biological Unit Coordinates (3nfl.pdb3.gz) 33 Kb
  • Biological Unit Coordinates (3nfl.pdb4.gz) 33 Kb
  • Biological Unit Coordinates (3nfl.pdb5.gz) 66 Kb
  • Biological Unit Coordinates (3nfl.pdb6.gz) 65 Kb
  • CSU: Contacts of Structural Units for 3NFL
  • Structure Factors (744 Kb)
  • Retrieve 3NFL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NFL from S2C, [Save to disk]
  • Re-refined 3nfl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NFL 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 3NFL
  • 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 3NFL, from MSDmotif at EBI
  • Fold representative 3nfl from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nfl_G] [3nfl_A] [3nfl_C] [3nfl_B] [3nfl] [3nfl_H] [3nfl_E] [3nfl_D] [3nfl_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NFL: [PDZ ] by SMART
  • Other resources with information on 3NFL
  • Community annotation for 3NFL at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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