2VSP Transport Protein date Apr 28, 2008
title Crystal Structure Of The Fourth Pdz Domain Of Pdz Domain- Containing Protein 1
authors W.W.Yue, N.Shafqat, E.S.Pilka, C.Johansson, J.W.Murray, J.Elkins, A.Roos, C.Cooper, C.Phillips, E.Salah, F.Von Delft, D.Doyle, A.Edwards, M.Wikstrom, C.Arrowsmith, C.Bountra, U.Oppermann
compound source
Molecule: Pdz Domain-Containing Protein 1
Chain: A, B, C, D
Fragment: Fourth Pdz Domain, Residues 375-459
Synonym: Cftr-Associated Protein Of 70 Kda, Napi Cotransporter C-Terminal-Associated Protein, Napi-Cap1, Na+H+ Exchanger Regulatory Factor 3, Sodium-Hydrogen Exchanger Regulatory Factor 3;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-R3-Prare2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pnic28-Bsa4
Other_details: Mgc
symmetry Space Group: H 3
R_factor 0.215 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.327 99.327 97.114 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.60 Å
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (109 Kb) [Save to disk]
  • Biological Unit Coordinates (2vsp.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (2vsp.pdb2.gz) 25 Kb
  • Biological Unit Coordinates (2vsp.pdb3.gz) 27 Kb
  • Biological Unit Coordinates (2vsp.pdb4.gz) 26 Kb
  • CSU: Contacts of Structural Units for 2VSP
  • Likely Quarternary Molecular Structure file(s) for 2VSP
  • Structure Factors (257 Kb)
  • Retrieve 2VSP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VSP from S2C, [Save to disk]
  • Re-refined 2vsp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VSP 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 2VSP
  • 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 2VSP, from MSDmotif at EBI
  • Fold representative 2vsp from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vsp_A] [2vsp_B] [2vsp_C] [2vsp_D]
  • SWISS-PROT database: [Q5T2W1]
  • Domain organization of [NHRF3_HUMAN] by SWISSPFAM
  • Domain found in 2VSP: [PDZ ] by SMART
  • Alignments of the sequence of 2VSP with the sequences similar proteins can be viewed for 2VSP's classification [NHRF3_HUMAN] 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 [NHRF3_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2VSP
  • Community annotation for 2VSP 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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