4NGD Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having 5'-p and UU-3' ends (1.95 Angstrom resolution) date
authors Tian, Y., Simanshu, D.K., Patel, D.J.
compound source
symmetry
R_factor
R_Free 0.2042
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.96
ligand PEG, SO4 enzyme
Primary referenceA Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer., Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ, Mol Cell. 2014 Feb 20;53(4):606-16. doi: 10.1016/j.molcel.2014.01.003. Epub 2014 , Jan 30. PMID:24486018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (164 Kb) [Save to disk]
  • Biological Unit Coordinates (4ngd.pdb1.gz) 172 Kb
  • Biological Unit Coordinates (4ngd.pdb2.gz) 316 Kb
  • LPC: Ligand-Protein Contacts for 4NGD
  • CSU: Contacts of Structural Units for 4NGD
  • Structure Factors (211 Kb)
  • Retrieve 4NGD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4NGD from S2C, [Save to disk]
  • Re-refined 4ngd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4NGD 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 4NGD
  • 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 4NGD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4ngd_A] [4ngd] [4ngd_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4NGD: [PAZ ] by SMART
    • Other resources with information on 4NGD
  • Community annotation for 4NGD at PDBWiki (http://pdbwiki.org)

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