Structure of PDB 5ndw Chain M1 Binding Site BS01

Receptor Information

>5ndw Chain M1 (length=169) Species: 559292 (Saccharomyces cerevisiae S288C)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

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): K16 V18 N20 S22 G24 S48 A50 R51 Y52 F57 I65 H68 N95 S97 A98 T99 N101 G103 F104 G105 G124 M125 D126 Y128 K142 K174
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 A45 R46 Y47 F52 I60 H63 N90 S92 A93 T94 N96 G98 F99 G100 G119 M120 D121 Y123 K137 K169

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• 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: Q3E757|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)