Structure of PDB 5ndw Chain O8 Binding Site BS01

Receptor Information

>5ndw Chain O8 (length=77) Species: 559292 (Saccharomyces cerevisiae S288C)

AREITDIKQFLELTRRADVKTATVKINKKLNKAGKPFRQTKFKVRGSSSL
YTLVINDAGKAKKLIQSLPPTLKVNRL

Ligand information

>5ndw Chain 1 (length=3090)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccgaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguuugaug
cccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaa
ggucgggucgaacggccucuagugcagaucuuggugguaguagcaaauau
ucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaacag
caguuggacguggguuagucgauccuaagagauggggaagcuccguuuca
aaggccugauuuuaugcaggccaccaucgaaagggaauccgguuaagauu
ccggaaccuggauauggauucuucacgguaacguaacugaauguggagac
gucggcgcgagcccugggaggaguuaucuuuucuucuuaacagcuuauca
ccccggaauugguuuauccggagauggggucuuauggcuggaagaggcca
gcaccuuugcuggcuccggugcgcuugugacggcccgugaaaauccacag
gaaggaauaguuuucaugccaggucguacugauaaccgcagcaggucucc
aaggugaacagccucuaguugauagaauaauguagauaagggaagucggc
aaaauagauccguaacuucgggauaaggauuggcucuaagggucgacgau
caacuuagaacugguacggacaaggggaaucugacugucuaauuaaaaca
uagcauugcgauggucagaaagugauguugacgcaaugugauuucugccc
agugcucugaaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaau
uagugacgcgcaugaauggauuaacgagauucccacugucccuaucuacu
aucuagcgaaaccacagccaagggaacgggcuuggcagaaucagcgggga
aagaagacccuguugagcuugacucuaguuugacauugugaagagacuuu
cuuuacuuauucaaugaagcggagcuggaauucauuuuccacguucuagc
auucaaggucccauucggggcugauccggguugaagacauugucaggugg
ggaguuuggcuggggcggcacaucuguuaaacgauaacgcagauguccua
aggggggcucauggagaacagaaaucuccaguagaacaaaaggguaaaag
cccccuugauuuugauuuucagugugaauacaaaccaugaaaguguggcc
uaucgauccuuuagucccucggaauuugaggcuagaggugccagaaaagu
uaccacagggauaacuggcuuguggcagucaagcguucauagcgacauug
cuuuuugauucuucgaugucggcucuuccuaucauaccgaagcagaauuc
gguaagcguuggauuguucacccacuaauagggaacgugagcuggguuua
gaccgucgugagacagguuaguuuuacccuacugaugaauguuaccgcaa
uaguaauugaacuuaguacgagaggaacaguucauucggauaauugguuu
uugcggcugucugaucaggcauugccgcgaagcuaccauccgcuggauua
uggcugaacgccucuaagucagaauccaugcuagaacgcggugauuucuu
ugcuccacacaauauagauggauacgaauaaggcguccuuguggcgucgc
ugaaccauagcaggcuagcaacggugcacuuggcggaaaggccuugggug
cuugcuggcgaauugcaaugucauuuugcguggggauaaaucauuuguau
acgacuuagauguacaacgggguauuguaagcaguagaguagccuuguug
uuacgaucugcugagauuaagccuuuguugucugauuugu

........................<<<<<<.....<......>......>
>>>>.>.........<<....>>..<<<<<......<<.....>>.....
>>>>>..[[[..<<.......<<.<<<<<<...>>>>>>.>>.......>
>....<<<<<<<.<<<<<<<<<<<<<<<<<<<<.....<<<<......>>
>>.(.......<<<......)>>>....>>>>>>>>..>>>>>>>>....
>>>>>>>>>>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<......>>>............
......................<<<<<.<<<<<......<<<<<<<.<<<
<<<<<<<<<<<<.....<<<<<<<<<......<<<<<......>>>>>..
.....>>>>>>>.>.>.>>>>>.>>>>>>>>>>........<<<....>>
>.....>>>>>>>.....>>>>>.>>>>>..<<<<........>>>><<<
<<<....<<<<<<.<<<<<<..<<<...<<<<.....>>>>...>>>...
<<....>>.......<<<<<..<<<<<....>>>>>...>>>>>.<<<<<
<<<...<<....>>...>>>.>>>.>>....>>>>>>.>>>>>>..<<.<
..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>>
.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>>
...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<.
<<<....>>>(><<<<<<<<<<...<<<.<<<<<<<.....<<<....<<
<....<<<<...<..<<.......>>..>.>>>>....>>>..>.>>...
..>>>>>...<<<<.<<<<.........>>>>.>>>>.....>>>>>.>>
>>>>>>.>>).<<<<.<<<<<.....>>>>>.>>>>....<<<......>
>>...<<<<<<<..<<<<(((.....<<<<<<......<..........<
<<.<<<<<<<<<<.......<<<<..>>>>...>>>>>>>>>>>>>....
......))).>....>>>>>>.>>>>..>>>>>>><<<<<<<<<.....>
>>>>>>>>....>>>>>>..<<<<<<<<.<<......<<<<.<<<<....
>>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.....<
<<<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<.
....>>.>>>>>>....((<<<<<<...<<....<<<....>>>......
..<<<<<<<<...>>.>>>>>>....>>....>>...<<<<<........
>>>>>))<<<<.<<<<<<<.....<<<....>>>.......<<<<<<...
<<<<.<<<<<<<.<<<<<<<<<<..{{{..>>>>>><...<<<<<....<
<<<<<....<<<.....>>>....>>>>>>.....>>>>>....><<<<<
<<......>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>.
.........>>>..>>>>>>>>>>>>..>>.....<<......>>>>>>>
.<<<<.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........
......<<<<<...............>>>>><<.<<<<<<<<<<...>>>
>..>>>>>>.>>............<<<<<<<<<..<<<.........>>>
..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<.
.<<<<<<.....<<.....<<<<....>>>>.....>>..>>>>..>>>>
><<<<<<.......>>>>>>........<...........<<<<<.....
..>>>>>.....>.....>>....>>.>>>>>>>.....>>.>>>>>>>.
.>>>>>>....>>....<<<<<........>>>>>....[[[[[..{{{.
{{......[[[[.{{[[[[..<<<<<.<<<<<<<<..<<<<<<<<<.>>>
>>>>>>...<<<<<.....<<<<..<<<<<......>>>>>.........
......<<<<<......>>>>>..>>>>..>>>>>.....>>>>>>>>..
>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<..
.<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....>
>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>))
).......((((((..((((.>>>>>>))))))))))..........]]]
]..}}]]]].......<<.<...<<<<<<...<<.......>>...>>>>
>>....>.>.>.......<<<<<.<<<<<<..<.<<<<<<<......>>>
>>>>...>.<<<.........>>>.....>>>>>..>...>>>.>>....
<<<<<<<....>>>.>>>>....}}..}}}.]]]]]....<<<<<<<<..
<<<<...<<<<<<...............>>>>>>..<<<<<...<<<<..
..<<<<<<<<<.}}}..>>>>..>>>>>...>>>>..>>>>>.<<<<...
<<<<<...........>>>>>...>>>>.>>>>....>>>>>>>>.....
..<<<<<<.<<<.<<....<<..........<<<<<<.....>>>>>>..
....>>.......<<<<<<...<<<<<.<..<<<......>>>..>.>>>
>>.>>>>>>.............>>.>>>.>>>>>>..<<<<<.<......
.......>.....<<<<<<<<<.<<<....<<<<....<<<<<......>
>>>>...>>>>...>>>....>>>>.>>>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ndw Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): A2 R3 E4 R17 D19 K26 K42 K44 R46 S48 S49 S50 L51 T53
• Binding residue (residue number reindexed from 1): A1 R2 E3 R16 D18 K25 K41 K43 R45 S47 S48 S49 L50 T52

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0022618 protein-RNA complex assembly

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P49167|RL38_YEAST Large ribosomal subunit protein eL38 (Gene Name=RPL38)