4PKD U1-70k in complex with U1 snRNA stem-loops 1 and U1-A RRM in complex with stem-loop 2 date
authors Oubridge, C., Kondo, Y., Roon, A.M.van., Nagai, K.
compound source
symmetry
R_factor
R_Free 0.25791
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.50
ligand GTP, IMD, MG enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


Primary referenceCrystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition., Kondo Y, Oubridge C, van Roon AM, Nagai K, Elife. 2015 Jan 2;4. doi: 10.7554/eLife.04986. PMID:25555158
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (73 Kb) [Save to disk]
  • Biological Unit Coordinates (4pkd.pdb1.gz) 66 Kb
  • LPC: Ligand-Protein Contacts for 4PKD
  • CSU: Contacts of Structural Units for 4PKD
  • Structure Factors (907 Kb)
  • Retrieve 4PKD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4PKD from S2C, [Save to disk]
  • Re-refined 4pkd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4PKD 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 4PKD
  • 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 4PKD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4pkd] [4pkd_V] [4pkd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4PKD: [RRM ] by SMART
    • Other resources with information on 4PKD
  • Community annotation for 4PKD at PDBWiki (http://pdbwiki.org)

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