4DR2 Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with multiple copies of paromomycin molecules 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 0.2109
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.25
ligand 0TD, 2MG, 4OC, 5MC, 7MG, M2G, MA6, MG, PAR, PSU, UR3, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


E


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] (2236 Kb) [Save to disk]
  • Biological Unit Coordinates (4dr2.pdb1.gz) 2188 Kb
  • LPC: Ligand-Protein Contacts for 4DR2
  • CSU: Contacts of Structural Units for 4DR2
  • Structure Factors (4294 Kb)
  • Retrieve 4DR2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DR2 from S2C, [Save to disk]
  • Re-refined 4dr2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DR2 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 4DR2
  • 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 4DR2, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dr2_S] [4dr2_N] [4dr2_F] [4dr2_G] [4dr2_Q] [4dr2] [4dr2_M] [4dr2_E] [4dr2_A] [4dr2_L] [4dr2_R] [4dr2_B] [4dr2_D] [4dr2_C] [4dr2_H] [4dr2_O] [4dr2_P] [4dr2_J] [4dr2_I] [4dr2_T] [4dr2_K] [4dr2_U]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4DR2: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
  • Other resources with information on 4DR2
  • Community annotation for 4DR2 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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