6C4H Ribosomal Protein Rna date Jan 12, 2018
title Conformation Of Methylated Ggq In The Peptidyl Transferase C During Translation Termination (Ptc Region)
authors F.Zeng, H.Jin
compound source
Molecule: 23s Rrna
Chain: A
 Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L2
Chain: C
Synonym: Large Ribosomal Subunit Protein Ul2
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L3
Chain: D
Synonym: Large Ribosomal Subunit Protein Ul3
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L16
Chain: N
Synonym: Large Ribosomal Subunit Protein Ul16
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: 50s Ribosomal Protein L27
Chain: X
Synonym: Large Ribosomal Subunit Protein Bl27
Organism_scientific: Escherichia Coli
Organism_taxid: 562

Molecule: P-Site Trna Fmet
Chain: x
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Peptide Chain Release Factor Rf2
Chain: v
Synonym: Rf-2
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Prfb, Supk, B2891, Jw5847
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.10 Å
ligand 1MG, 2MA, 2MG, 5MC, 5MU, G7M, MEQ, MG, OMC, OMG, OMU, PSU enzyme
Gene
Ontology
ChainFunctionProcessComponent
C


D


N


X


v


Primary referenceConformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination., Zeng F, Jin H, Sci Rep. 2018 Feb 5;8(1):2349. doi: 10.1038/s41598-018-20107-8. PMID:29403017
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (319 Kb) [Save to disk]
  • Biological Unit Coordinates (6c4h.pdb1.gz) 297 Kb
  • LPC: Ligand-Protein Contacts for 6C4H
  • CSU: Contacts of Structural Units for 6C4H
  • Retrieve 6C4H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6C4H from S2C, [Save to disk]
    • View 6C4H 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 6C4H
  • 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: [6c4h_D] [6c4h_X] [6c4h_v] [6c4h_x] [6c4h_C] [6c4h_N] [6c4h_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6C4H
  • Community annotation for 6C4H at PDBWiki (http://pdbwiki.org)

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