4OHW Rna Binding Protein date Jan 18, 2014
title C. Elegans Clp1 Bound To Atp, And Mn2+(Atp-Bound State)
authors A.Dikfidan, B.Loll, C.Zeymer, T.Clausen, A.Meinhart
compound source
Molecule: Protein Clpf-1
Chain: A
Engineered: Yes
Organism_scientific: Caenorhabditis Elegans
Organism_common: Nematode
Organism_taxid: 6239
Gene: Clpf-1, F59a2.4
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 31
R_factor 0.202 R_Free 0.241
length a length b length c angle alpha angle beta angle gamma
99.340 99.340 40.800 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand 2PE, ATP, MN enzyme

Primary referenceRNA specificity and regulation of catalysis in the eukaryotic polynucleotide kinase clp1., Dikfidan A, Loll B, Zeymer C, Magler I, Clausen T, Meinhart A, Mol Cell. 2014 Jun 19;54(6):975-86. doi: 10.1016/j.molcel.2014.04.005. Epub 2014 , May 8. PMID:24813946
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (140 Kb) [Save to disk]
  • Biological Unit Coordinates (4ohw.pdb1.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 4OHW
  • CSU: Contacts of Structural Units for 4OHW
  • Structure Factors (376 Kb)
  • Retrieve 4OHW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4OHW from S2C, [Save to disk]
  • Re-refined 4ohw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4OHW 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 4OHW
  • 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 4OHW, from MSDmotif at EBI
  • Fold representative 4ohw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ohw_A] [4ohw]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4OHW
  • Community annotation for 4OHW at PDBWiki (http://pdbwiki.org)

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