Structure of PDB 5ndw Chain n6 Binding Site BS01

Receptor Information

>5ndw Chain n6 (length=122) Species: 559292 (Saccharomyces cerevisiae S288C)

AKQSLDVSSDRRKARKAYFTAPSSQRRVLLSAPLSKELRAQYGIKALPIR
RDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGASVPINLHP
SKLVITKLHLDKDRKALIQRKG

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): A2 K3 Q4 S5 V8 S9 S10 R12 K14 A15 R16 Y19 V29 L30 S32 P34 R40 K46 R60 G61 S62 K87 K89 V90 N91 H100 S102 K103 R121 K122
• Binding residue (residue number reindexed from 1): A1 K2 Q3 S4 V7 S8 S9 R11 K13 A14 R15 Y18 V28 L29 S31 P33 R39 K45 R59 G60 S61 K86 K88 V89 N90 H99 S101 K102 R120 K121

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0032991 protein-containing complex
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P05743|RL26A_YEAST Large ribosomal subunit protein uL24A (Gene Name=RPL26A)