Structure of PDB 5ndw Chain O4 Binding Site BS01

Receptor Information

>5ndw Chain O4 (length=112) Species: 559292 (Saccharomyces cerevisiae S288C)

AQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSAL
QGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIV
KKVVKEQTEAAK

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 R4 V5 F7 R8 R9 R10 N11 P12 Y13 N14 T15 S17 K19 V22 K24 T25 P26 G27 L30 R31 Q33 K36 K37 L38 T40 R41 P42 K43 G45 Q52 G53 I54 S55 T56 R58 P59 R60 Y62 A63 S66 K67 T68 K70 T71 S73 R74 Y76 G77 G78 S79 R80 N83 R88 R91 A92 I95 E96 Q98
• Binding residue (residue number reindexed from 1): A1 R3 V4 F6 R7 R8 R9 N10 P11 Y12 N13 T14 S16 K18 V21 K23 T24 P25 G26 L29 R30 Q32 K35 K36 L37 T39 R40 P41 K42 G44 Q51 G52 I53 S54 T55 R57 P58 R59 Y61 A62 S65 K66 T67 K69 T70 S72 R73 Y75 G76 G77 S78 R79 N82 R87 R90 A91 I94 E95 Q97

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5ndw, PDBe:5ndw, PDBj:5ndw
• PDBsum: 5ndw
• PubMed: 29208708
• UniProt: P87262|RL34A_YEAST Large ribosomal subunit protein eL34A (Gene Name=RPL34A)