5TPY Rna date Oct 21, 2016
title Crystal Structure Of An Exonuclease Resistant Rna From Zika
authors B.M.Akiyama, H.M.Laurence, A.R.Massey, D.A.Costantino, X.Xie, Y.Y Y.Shi, J.C.Nix, J.D.Beckham, J.S.Kieft
compound source
Molecule: Rna (71-Mer)
Chain: A
Engineered: Yes
Synthetic: Yes
Organism_scientific: Zika Virus
Organism_taxid: 64320
Other_details: Mr766-Niid
symmetry Space Group: P 64 2 2
R_factor 0.191 R_Free 0.218
length a length b length c angle alpha angle beta angle gamma
111.679 111.679 90.826 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.81 Å
ligand HEZ, MG enzyme
Primary referenceZika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease., Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS, Science. 2016 Dec 2;354(6316):1148-1152. Epub 2016 Nov 10. PMID:27934765
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (5tpy.pdb1.gz) 122 Kb
  • LPC: Ligand-Protein Contacts for 5TPY
  • CSU: Contacts of Structural Units for 5TPY
  • Structure Factors (224 Kb)
  • Retrieve 5TPY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5TPY from S2C, [Save to disk]
  • Re-refined 5tpy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5TPY 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 5TPY
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5tpy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5tpy_A] [5tpy]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5TPY
  • Community annotation for 5TPY at PDBWiki (http://pdbwiki.org)

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