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 5 (length=3080)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccgaccggccgaaugaacuagcccugaaa
auggauggcgcucaagcguguuaccuauacucuaccgucaggguugaugc
ccugacgaguaggcaggcguggaggucagugacgaagccuagaccguaag
gucgggucgaacggccucuagugcagaucuuggugguaguagcaaauauu
caaaugagaacuuugaagacugaaguggggaaagguuccacgucaacagc
aguuggacguggguuagucgauccuaagagauggggaagcuccguuucaa
aggccuguaugcaggccaccaucgaaagggaauccgguuaagauuccgga
accuggauauggauucuucacgguaacguaacugaauguggagacgucgg
cgcgagcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccg
gaauugguuuauccggagauggggucuuauggcuggaagaggccagcacg
cuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaaua
guuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaac
agccucuaguugauagaauaauguagauaagggaagucggcaaaauagau
ccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuuag
aacugguacggacaaggggaaucugacugucuaauuaaaacauagcauug
cgauggucagaaagugauguugacgcaaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggauuaacgagauucccacugucccuaucuacuaucuagcg
aaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaagac
ccuguugagcuugacucuaguuugacauugugaagaguuucuuuacuuau
ucaaugaagcggagcuggaauucauuuuccacguucuagcauucaagguc
ccauucggggcugauccggguugaagacauugucagguggggaguuuggc
uggggcggcacaucuguuaaacgauaacgcagauguccuaaggggggcuc
auggagaacagaaaucuccaguagaacaaaaggguaaaagcccccuugau
uuugauuuucagugugaauacaaaccaugaaaguguggccuaucgauccu
uuagucccucggaauuugaggcuagaggugccagaaaaguuaccacaggg
auaacuggcuuguggcagucaagcguucauagcgacauugcuuuuugauu
cuucgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguu
ggauuguucacccacuaauagggaacgugagcuggguuuagaccgucgug
agacagguuaguuuuacccuacugaugaauguuaccgcaauaguaauuga
acuuaguacgagaggaacaguucauucggauaauugguuuuugcggcugu
cugaucaggcauugccgcgaagcuaccauccgcuggauuauggcugaacg
ccucuaagucagaauccaugcuagaacgcggugauuucuuugcuccacac
aauauagauggauacgaauaaggcguccuuguggcgucgcugaaccauag
caggcuagcaacggugcacuuggcggaaaggccuugggugcuugcuggcg
aauugcaaugucauuuugcguggggauaaaucauuuguauacgacuuaga
uguacaacgggguauuguaagcaguagaguagccuuguuguuacgaucug
cugagauuaagccuuuguugucugauuugu

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

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 T56 F57 I59 H68 R94 N95 S97 A98 T99 N101 G103 F104 G105 I106 D107 G124 M125 D126 Y128 V130 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 A45 R46 Y47 T51 F52 I54 H63 R89 N90 S92 A93 T94 N96 G98 F99 G100 I101 D102 G119 M120 D121 Y123 V125 K137

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)