4GKK Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin date
authors Cantara, W.A., IV, F.V.Murphy., Spears, J.L., Demirci, H., Agris, P.F.
compound source
symmetry
R_factor
R_Free 0.2359
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.20
ligand MG, PAR, RSQ, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
B


C


D


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F


G


H


I


J


K


L


M


N


O


P


Q


R


S


T


V


Primary referenceExpanded use of sense codons is regulated by modified cytidines in tRNA., Cantara WA, Murphy FV 4th, Demirci H, Agris PF, Proc Natl Acad Sci U S A. 2013 Jun 18. PMID:23781103
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2144 Kb) [Save to disk]
  • Biological Unit Coordinates (4gkk.pdb1.gz) 2132 Kb
  • LPC: Ligand-Protein Contacts for 4GKK
  • CSU: Contacts of Structural Units for 4GKK
  • Structure Factors (4139 Kb)
  • Retrieve 4GKK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4GKK from S2C, [Save to disk]
  • Re-refined 4gkk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4GKK 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 4GKK
  • 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 4GKK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4gkk_I] [4gkk_J] [4gkk_M] [4gkk_G] [4gkk_H] [4gkk_C] [4gkk_B] [4gkk_A] [4gkk_O] [4gkk_D] [4gkk_X] [4gkk_K] [4gkk_N] [4gkk_S] [4gkk_V] [4gkk_T] [4gkk_L] [4gkk_W] [4gkk_Q] [4gkk_R] [4gkk_F] [4gkk_E] [4gkk_P] [4gkk]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4GKK: [KH] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART
    • Other resources with information on 4GKK
  • Community annotation for 4GKK at PDBWiki (http://pdbwiki.org)

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