Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

This is a large structure.

Summary for 5NDK

Descriptor16S ribosomal RNA, 50S ribosomal protein L18, 50S ribosomal protein L23, ... (56 entities in total)
Functional Keywordstranslation, ribosome, 3s, 50s, 70s, trna, mrna, bacteria, rna-protein complex, inhibitor, antibiotic, aminoglycoside
Biological sourceThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Total number of polymer chains108
Total molecular weight4521807.35
Prokhorova, I.,Djumagulov, M.,Urzhumtsev, A.,Yusupov, M.,Yusupova, G. (deposition date: 2017-03-08, release date: 2017-12-13, Last modification date: 2017-12-27)
Primary citation
Prokhorova, I.,Altman, R.B.,Djumagulov, M.,Shrestha, J.P.,Urzhumtsev, A.,Ferguson, A.,Chang, C.T.,Yusupov, M.,Blanchard, S.C.,Yusupova, G.
Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Proc. Natl. Acad. Sci. U.S.A., 114:E10899-E10908, 2017
PubMed: 29208708 (PDB entries with the same primary citation)
DOI: 10.1073/pnas.1715501114
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.254171.8%21.4%7.4%0.45MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5ndk
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Molmil generated image of 5ndk
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Molmil generated image of 5ndk
rotated about y axis by 90°