4PRF A Second Look at the HDV Ribozyme Structure and Dynamics. date
authors Kapral, G.J., Jain, S., Noeske, J., Doudna, J.A., Richardson, D.C., Richardson, J.S.
compound source
symmetry
R_factor
R_Free 0.2518
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.40
ligand SR enzyme
note 4PRF supersedes 1VC7
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNew tools provide a second look at HDV ribozyme structure, dynamics and cleavage., Kapral GJ, Jain S, Noeske J, Doudna JA, Richardson DC, Richardson JS, Nucleic Acids Res. 2014 Oct 17. pii: gku992. PMID:25326328
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (4prf.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 4PRF
  • CSU: Contacts of Structural Units for 4PRF
  • Structure Factors (136 Kb)
  • Retrieve 4PRF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PRF from S2C, [Save to disk]
  • Re-refined 4prf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4PRF 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 4PRF
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4PRF, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4prf_B] [4prf] [4prf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4PRF: [RRM ] by SMART
  • Other resources with information on 4PRF
  • Community annotation for 4PRF at PDBWiki (http://pdbwiki.org)

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