4DR6 Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound date
authors Demirci, H., IV, F.Murphy., Murphy, E., Gregory, S.T., Dahlberg, A.E., Jogl, G.
compound source
symmetry
R_factor
R_Free 0.1918
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.30
ligand 0TD, 2MG, 4OC, 5MC, 7MG, M2G, MA6, MG, PSU, SRY, UR3, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
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F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


U


Primary referenceA structural basis for streptomycin-induced misreading of the genetic code., Demirci H, Murphy F 4th, Murphy E, Gregory ST, Dahlberg AE, Jogl G, Nat Commun. 2013 Jan 15;4:1355. doi: 10.1038/ncomms2346. PMID:23322043
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2333 Kb) [Save to disk]
  • Biological Unit Coordinates (4dr6.pdb1.gz) 2277 Kb
  • LPC: Ligand-Protein Contacts for 4DR6
  • CSU: Contacts of Structural Units for 4DR6
  • Structure Factors (1758 Kb)
  • Retrieve 4DR6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DR6 from S2C, [Save to disk]
  • Re-refined 4dr6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DR6 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 4DR6
  • 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 4DR6, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dr6_F] [4dr6_M] [4dr6_A] [4dr6_S] [4dr6_R] [4dr6_K] [4dr6_E] [4dr6_W] [4dr6_B] [4dr6_H] [4dr6_O] [4dr6_D] [4dr6_U] [4dr6_a] [4dr6_C] [4dr6_b] [4dr6_T] [4dr6_N] [4dr6_Q] [4dr6_V] [4dr6_I] [4dr6_J] [4dr6_G] [4dr6] [4dr6_P] [4dr6_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DR6: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4DR6
  • Community annotation for 4DR6 at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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