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Structure of PDB 5ndj Chain 2I Binding Site BS01

Receptor Information >5ndj Chain 2I (length=116) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure] KRQVASGRAYIHASYNNTIVTITDPDGNPITWSSGGVIGYKGSRKGTPYA AQLAALDAAKKAMAYGMQSVDVIVRGTGAGREQAIRALQASGLQVKSIVD DTPVPHNGCRPKKKFR

Ligand information >5ndj Chain 13 (length=1508) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure] uuggagaguuugauccuggcucagggugaacgcuggcggcgugccuaaga caugcaagucgugcgggccgcggguccguggucagcggcggacgggugag uaacgcgugggugaccuacccggaagagggggacaacccggggaaacucg ggcuaaucccccauguggacccgccccuugggguguguccaaagggcuuu gcccgcuuccggaugggcccgcgucccaucagcuaguuggugggguaaug gcccaccaaggcgacgacggguagccggucugagaggauggccggccaca ggggcacugagacacgggccccacuccuacgggaggcagcaguuaggaau cuuccgcaaugggcgcaagccugacggagcgacgccgcuuggaggaagaa gcccuucgggguguaaacuccugaacccgggacgaaacccccgacgaggg gacugacgguaccgggguaauagcgccggccaacuccgugccagcagccg cgguaauacggagggcgcgagcguuacccggauucacugggcguaaaggg cguguaggcggccuggggcgucccaugugaaagaccacggcucaaccgug ggggagcgugggauacgcucaggcuagacggugggagagggugguggaau ucccggaguagcggugaaaugcgcagauaccgggaggaacgccgauggcg aaggcagccaccugguccacccgugacgcugaggcgcgaaagcgugggga gcaaaccggauuagauacccggguaguccacgcccuaaacgaugcgcgcu aggucucugggucuccugggggccgaagcuaacgcguuaagcgcgccgcc uggggaguacggccgcaaggcugaaacucaaaggaauugacgggggcccg cacaagcgguggagcaugugguuuaauucgaagcaacgcgaagaaccuua ccaggccuugacaugcuagggaacccgggugaaagccuggggugccccgc gaggggagcccuagcacaggugcugcauggccgucgucagcucgugccgu gagguguuggguuaagucccgcaacgagcgcaacccccgccguuaguugc cagcgguucggccgggcacucuaacgggacugcccgcgaaagcgggagga aggaggggacgacgucuggucagcauggcccuuacggccugggcgacaca cgugcuacaaugcccacuacaaagcgaugccacccggcaacggggagcua aucgcaaaaaggugggcccaguucggauuggggucugcaacccgacccca ugaagccggaaucgcuaguaaucgcggaucagccaugccgcggugaauac guucccgggccuuguacacaccgcccgucacgccaugggagcgggcucua cccgaagucgccgggagccuacgggcaggcgccgaggguagggcccguga cuggggcgaagucguaacaagguagcuguaccggaaggugcggcuggauc accuccuu .....<<<<..[.((((.>>>>.<<<<.<<<<<..<<<<<<<<..<..<< <.<<<..<<<..<<.<<<<<........>>>>>.>>>>>......<<... ....<<<<<<<<..<<...<<<<<<<.<<<<<....<<<<<......>>> >>.....>>>>>...<<<<<.<<<<<....>>>>>.>>>>>..<<<<... >>>>.>>>>>>>..>>>>>>>>>><<<....<<<..<<<<<<<<...... .>>>>>>>>>>>......>>>..<<<<<<<<....>>>>...>>>>.>>. <<<<<.<.........>>>>>>.<<<<....>>>>...>>>>>>>..... ...<<<....<<<<....>>>>..>>>..>>.>>>>>>..<<<<...... <<<<....>>>>.....>>>>....<<<<<........<<<<.....>>> >..........>>>>>......<<<<<(((...<<<<<.....<<.)))> >.......>>>>>>>>>>..>>>>>>>>>..........<<<((.....< <<<...<<<.<<<<<<<.<<<<<<<<<<......<<<<<<.....>>>>> >....>>>>>>>>..>>>>>>>>>...<<<<<<<<...<<<<<<<....< <<<<<<.<..<<<......>>>.....>.>>>>>>>...........<<. ...>>.>>>>>>>..>>>>>.>>>...>>>...>>>>....<<<<<<... <<...<<<<.........>>>>...>>>>>>>>..........<<<<<<. .<<<<<<<<<<...>>>>>>>>>>...<<..))>>.....>>>>>>.>>> .<<<......<<<<....>>>>....>>>..)))).]<<<<<.<<<<<<< .<<.<<<<<<..<<<<<<<<<<......<<........>>.......... <<<<<<<......<<<<<<<<..<<<<<<<....>>>>>>>...<<<... ...>>>..>>>>>>>>.<<<.<<<..<<<<<<.......<<<<<<<<<.. ..>>>..<<<<......>>>>..>>>>>>.....<<<<.<<<<<<<...< ...<<<.....>>>>.....>>>>>>>.....<<<<<....>>>>>.... ....>>>>.........>>>...>>>>>>>>>...>>>>>>>...>>.>> >>>>>>.....<<<<<<<.....<<<..<<..<<<<....>>>>..>>.. ..>>>.....>>>>>>>......<....<<<<<<<........>>>>>>> ....>.....>>>>>>....<<<<<<<..........>>>>>>>...... >>...>>>>>>>>>>.>>....<..<<.<.<<<<.<<<..<<<<<<<<<< <<<...<.<<<<....<<<....>>>.>>>>.>..>>>>>>>>>>>>>.. >>>.>>>>..>.>>...>.....<<<<<<<<<....>>>>>>>>>..... ........

Receptor-Ligand Complex Structure Global view Local view Structure summary [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] [Spin on] [Spin off] [Reset] [High quality] [Low quality] [White background] [Black background] PDB 5ndj Aminoglycoside interactions and impacts on the eukaryotic ribosome. Resolution 3.15 Å Binding residue (original residue number in PDB) Y20 N26 N27 I29 T31 N38 P39 W42 S44 G46 G52 S53 K55 R85 V114 H116 N117 G118 C119 R120 K122 K123 K124 Binding residue (residue number reindexed from 1) Y10 N16 N17 I19 T21 N28 P29 W32 S34 G36 G42 S43 K45 R75 V104 H106 N107 G108 C109 R110 K112 K113 K114

Enzymatic activity Enzyme Commision number ?

Gene Ontology Molecular Function GO:0003735 structural constituent of ribosome GO:0019843 rRNA binding

	Biological Process
GO:0006412	translation

	Cellular Component
GO:0005840	ribosome
GO:0022627	cytosolic small ribosomal subunit
GO:1990904	ribonucleoprotein complex

View graph for Molecular Function

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View graph for Cellular Component