3PDV Protein Binding date Oct 25, 2010
title Structure Of The Pdlim2 Pdz Domain In Complex With The C-Ter Peptide Extension Of Ns1
authors X.Li
compound source
Molecule: Pdz And Lim Domain Protein 2, C-Teminal Peptide F Nonstructural Protein 1;
Chain: A
Fragment: Pdz Domain
Synonym: Pdz-Lim Protein Mystique
Engineered: Yes
Other_details: Chimera Of Pdz And Lim Domain Protein 2 And Peptide From Nonstructural Protein 1
Organism_scientific: Homo Sapiens, Influenza A Virus
Organism_common: Human
Organism_taxid: 9606, 319102
Strain: Achickenhenan122004(H5n1)
Gene: Pdlim2, Ns1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: I 2 3
R_factor 0.198 R_Free 0.249
length a length b length c angle alpha angle beta angle gamma
81.917 81.917 81.917 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand NA enzyme
Primary referencePDlim2 selectively interacts with the PDZ binding motif of highly pathogenic avian H5N1 influenza A virus NS1., Yu J, Li X, Wang Y, Li B, Li H, Li Y, Zhou W, Zhang C, Wang Y, Rao Z, Bartlam M, Cao Y, PLoS One. 2011;6(5):e19511. Epub 2011 May 23. PMID:21625420
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (20 Kb) [Save to disk]
  • Biological Unit Coordinates (3pdv.pdb1.gz) 15 Kb
  • LPC: Ligand-Protein Contacts for 3PDV
  • CSU: Contacts of Structural Units for 3PDV
  • Structure Factors (73 Kb)
  • Retrieve 3PDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PDV from S2C, [Save to disk]
  • Re-refined 3pdv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PDV 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 3PDV
  • 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 3PDV, from MSDmotif at EBI
  • Fold representative 3pdv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pdv] [3pdv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3PDV: [PDZ ] by SMART
  • Other resources with information on 3PDV
  • Community annotation for 3PDV at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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