413D Rna date Jul 10, 1998
title A'-Form Rna Double Helix In The Single Crystal Structure Of R(Ugagcuucggcuc)
authors Y.Tanaka, S.Fujii, H.Hiroaki, T.Sakata, T.Tanaka, S.Uesugi, K. I.Tomita, Y.Kyogoku
compound source
Molecule: Rna (5'- R(Upgpapgpcpupupcpgpgpcpupc)-3');
Chain: A
Engineered: Yes
Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.182 R_Free 0.224
length a length b length c angle alpha angle beta angle gamma
38.490 32.300 38.760 90.00 117.56 90.00
method X-Ray Diffractionresolution 1.80 Å
note 413D supersedes 373D
Primary referenceA'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC)., Tanaka Y, Fujii S, Hiroaki H, Sakata T, Tanaka T, Uesugi S, Tomita K, Kyogoku Y, Nucleic Acids Res. 1999 Feb 15;27(4):949-55. PMID:9927725
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (10 Kb) [Save to disk]
  • Biological Unit Coordinates (413d.pdb1.gz) 9 Kb
  • CSU: Contacts of Structural Units for 413D
  • Likely Quarternary Molecular Structure file(s) for 413D
  • Retrieve 413D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 413D from S2C, [Save to disk]
  • View 413D 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 413D
  • 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
  • 3D motif for 413D, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Fold representative 413d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [413d_A] [413d]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 413D
  • Community annotation for 413D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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