5VP2

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

This is a large structure.

Summary for 5VP2

Descriptor23S Ribosomal RNA, 5S ribosomal RNA, 50S ribosomal protein L2, ... (61 entities in total)
Functional Keywordsmadumycin ii, streptogramin a, antibiotic, ribosome inhibitor, 70s ribosome, ribosome structure, inhibition of translation, peptidyl transferase center, ribosome
Biological sourceEscherichia coli
More
Total number of polymer chains112
Total molecular weight4571576.15
Authors
Osterman, I.A.,Khabibullina, N.F.,Komarova, E.S.,Kasatsky, P.,Kartsev, V.G.,Bogdanov, A.A.,Dontsova, O.A.,Konevega, A.L.,Sergiev, P.V.,Polikanov, Y.S. (deposition date: 2017-05-04, release date: 2017-06-28, Last modification date: 2019-06-26)
Primary citation
Osterman, I.A.,Khabibullina, N.F.,Komarova, E.S.,Kasatsky, P.,Kartsev, V.G.,Bogdanov, A.A.,Dontsova, O.A.,Konevega, A.L.,Sergiev, P.V.,Polikanov, Y.S.
Madumycin II inhibits peptide bond formation by forcing the peptidyl transferase center into an inactive state.
Nucleic Acids Res., 45:7507-7514, 2017
PubMed: 28505372 (PDB entries with the same primary citation)
DOI: 10.1093/nar/gkx413
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.8 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone 0.2788 0.8% 4.3% 4.4% 0.54MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
Download full validation reportDownload