4D25 Crystal structure of the Bombyx mori Vasa helicase (E339Q) in complex with RNA and AMPPNP date
authors Spinelli, P., Pillai, R.S., Kadlec, J., Cusack, S.
compound source
symmetry
R_factor
R_Free 0.20837
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.90
ligand ANP, GOL, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceRNA Clamping by Vasa Assembles a piRNA Amplifier Complex on Transposon Transcripts., Xiol J, Spinelli P, Laussmann MA, Homolka D, Yang Z, Cora E, Coute Y, Conn S, Kadlec J, Sachidanandam R, Kaksonen M, Cusack S, Ephrussi A, Pillai RS, Cell. 2014 Jun 4. pii: S0092-8674(14)00660-6. doi: 10.1016/j.cell.2014.05.018. PMID:24910301
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (148 Kb) [Save to disk]
  • Biological Unit Coordinates (4d25.pdb1.gz) 142 Kb
  • LPC: Ligand-Protein Contacts for 4D25
  • CSU: Contacts of Structural Units for 4D25
  • Structure Factors (653 Kb)
  • Retrieve 4D25 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4D25 from S2C, [Save to disk]
  • Re-refined 4d25 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4D25 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 4D25
  • 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 4D25, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4d25_A] [4d25] [4d25_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4D25: [DEXDc] [HELICc ] by SMART
    • Other resources with information on 4D25
  • Community annotation for 4D25 at PDBWiki (http://pdbwiki.org)

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