5NS3 Rna date Apr 25, 2017
title Crystal Structures Of Cy5 Cyanine Fluorophores Stacked Onto Double-Stranded Rna
authors Y.J.Liu, D.M.J.Lilley
compound source
Molecule: 50s Ribosomal Protein L5
Chain: A, B
Synonym: Tl4,Tthl5
Engineered: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
Gene: Rple, Rpl5
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Double-Stranded Rna
Chain: C, D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 21 21 2
R_factor 0.252 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.043 123.895 51.201 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal Structures of Cyanine Fluorophores Stacked onto the End of Double-Stranded RNA., Liu Y, Lilley DMJ, Biophys J. 2017 Dec 5;113(11):2336-2343. doi: 10.1016/j.bpj.2017.10.002. PMID:29211987
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (5ns3.pdb1.gz) 72 Kb
  • CSU: Contacts of Structural Units for 5NS3
  • Structure Factors (592 Kb)
  • Retrieve 5NS3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NS3 from S2C, [Save to disk]
  • View 5NS3 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 5NS3
  • 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
  • Fold representative 5ns3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ns3_C] [5ns3_A] [5ns3_B] [5ns3_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NS3
  • Community annotation for 5NS3 at PDBWiki (http://pdbwiki.org)

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