5DHC Rna date Aug 30, 2015
title Cooperativity And Downstream Binding In Rna Replication
authors W.Zhang, A.C.Fahrenbach, C.P.Tam, J.W.Szostak
compound source
Molecule: Rna (5'-R((Lcc)P(Lcc)P(Lca)P(Lcg) Papcpupupapapgpupcpu)-3');
Chain: A, B, C, D
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 3
R_factor 0.170 R_Free 0.195
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.107 43.107 83.245 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.55 Å
ligand 5GP, LCA, LCC, LCG, MG enzyme
Primary referenceUnusual Base-Pairing Interactions in Monomer-Template Complexes., Zhang W, Tam CP, Wang J, Szostak JW, ACS Cent Sci. 2016 Dec 28;2(12):916-926. doi: 10.1021/acscentsci.6b00278. Epub, 2016 Nov 2. PMID:28058281
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (5dhc.pdb1.gz) 18 Kb
  • Biological Unit Coordinates (5dhc.pdb2.gz) 18 Kb
  • LPC: Ligand-Protein Contacts for 5DHC
  • CSU: Contacts of Structural Units for 5DHC
  • Structure Factors (456 Kb)
  • Retrieve 5DHC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DHC from S2C, [Save to disk]
  • Re-refined 5dhc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DHC 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 5DHC
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dhc_D] [5dhc_C] [5dhc_A] [5dhc_B] [5dhc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5DHC
  • Community annotation for 5DHC at PDBWiki (http://pdbwiki.org)

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