2QPA Protein Transport date Jul 23, 2007
title Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Ad
authors J.Xiao, Z.Xu
compound source
Molecule: Vacuolar Protein Sorting-Associated Protein 4
Chain: A, B, C
Fragment: Residues: 83-437
Synonym: Protein End13, Doa4-Independent Degradation Protei Vacuolar Protein-Targeting Protein 10;
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Vps4, Csc1, Did6, End13, Grd13, Vpl4, Vpt10
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psj3
symmetry Space Group: P 21 21 21
R_factor 0.255 R_Free 0.305
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.630 120.640 157.330 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand ADP, PO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural characterization of the ATPase reaction cycle of endosomal AAA protein Vps4., Xiao J, Xia H, Yoshino-Koh K, Zhou J, Xu Z, J Mol Biol. 2007 Nov 30;374(3):655-70. Epub 2007 Sep 29. PMID:17949747
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (2qpa.pdb1.gz) 46 Kb
  • Biological Unit Coordinates (2qpa.pdb2.gz) 45 Kb
  • Biological Unit Coordinates (2qpa.pdb3.gz) 44 Kb
  • LPC: Ligand-Protein Contacts for 2QPA
  • CSU: Contacts of Structural Units for 2QPA
  • Likely Quarternary Molecular Structure file(s) for 2QPA
  • Structure Factors (480 Kb)
  • Retrieve 2QPA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2QPA from S2C, [Save to disk]
  • Re-refined 2qpa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2QPA 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 2QPA
  • 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
  • 3D motif for 2QPA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2qpa_C] [2qpa_B] [2qpa_A] [2qpa]
  • SWISS-PROT database: [P52917]
  • Domain organization of [VPS4_YEAST] by SWISSPFAM
  • Domain found in 2QPA: [AAA ] by SMART
  • Other resources with information on 2QPA
  • Community annotation for 2QPA 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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