6YML Rna date Apr 08, 2020
title Crystal Structure Of The Sam-Sah Riboswitch With Decarboxyla
authors L.Huang, D.M.J.Lilley
compound source
Molecule: Chains: A,C
Chain: A, C
Engineered: Yes
 Synthetic: Yes
Organism_scientific: Roseobacter Sp.
Organism_taxid: 1907202

Molecule: Chains: B,D
Chain: B, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Roseobacter Sp.
Organism_taxid: 1907202
symmetry Space Group: P 3 1 2
R_factor 0.198 R_Free 0.233
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.218 86.218 75.395 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.17 Å
ligand AMP, CBV, DSH, SO4 enzyme
Primary referenceCrystal structure and ligand-induced folding of the SAM/SAH riboswitch., Huang L, Liao TW, Wang J, Ha T, Lilley DMJ, Nucleic Acids Res. 2020 Jul 27;48(13):7545-7556. doi: 10.1093/nar/gkaa493. PMID:32520325
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (70 Kb) [Save to disk]
  • Biological Unit Coordinates (6yml.pdb1.gz) 33 Kb
  • Biological Unit Coordinates (6yml.pdb2.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 6YML
  • CSU: Contacts of Structural Units for 6YML
  • Structure Factors (659 Kb)
  • Retrieve 6YML in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6YML from S2C, [Save to disk]
    • View 6YML 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 6YML
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6yml_A] [6yml_C] [6yml_D] [6yml_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6YML
  • Community annotation for 6YML at PDBWiki (http://pdbwiki.org)

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