3B5S Rna date Oct 26, 2007
title Minimally Hinged Hairpin Ribozyme Incorporates A38dap Mutati O-Methyl Modification At The Active Site
authors C.Macelrevey, J.Krucinska, J.E.Wedekind
compound source
Molecule: Loop A Substrate Strand
Chain: A
Engineered: Yes
Other_details: 2'-O-Methyl Modification At Residue 5
 Synthetic: Yes
Other_details: Solid-Phase Synthesis At Keck Institute, Yal

Molecule: 29-Mer Loop A And Loop B Ribozyme Strand
Chain: B
Engineered: Yes
Other_details: Synthetic Polyethylene Glycol Linker At Hing 14;
Synthetic: Yes
Other_details: Solid Phase Chemical Synthesis At Dharmacon, Colorado;

Molecule: Loop B S-Turn Strand
Chain: C
Engineered: Yes
Mutation: Yes
Synthetic: Yes
Other_details: Solid Phase Chemical Synthesis At Dharmacon,
symmetry Space Group: P 61 2 2
R_factor 0.223 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.500 93.500 133.420 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.25 Å
ligand A2M, N6G, NCO, S9L, SO4 enzyme
Primary referenceStructural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme., MacElrevey C, Salter JD, Krucinska J, Wedekind JE, RNA. 2008 Aug;14(8):1600-16. Epub 2008 Jul 2. PMID:18596253
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (3b5s.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 3B5S
  • CSU: Contacts of Structural Units for 3B5S
  • Likely Quarternary Molecular Structure file(s) for 3B5S
  • Structure Factors (224 Kb)
  • Retrieve 3B5S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B5S from S2C, [Save to disk]
  • Re-refined 3b5s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3B5S 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 3B5S
  • 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 3B5S, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b5s_A] [3b5s_B] [3b5s] [3b5s_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3B5S
  • Community annotation for 3B5S 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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