Structure of PDB 5obm Chain N1 Binding Site BS01

Receptor Information

>5obm Chain N1 (length=159) Species: 559292 (Saccharomyces cerevisiae S288C)

GKSHGYRSRTRYMFQRDFRKHGAVHLSTYLKVYKVGDIVDIKANGSIQKG
MPHKFYQGKTGVVYNVTKSSVGVIINKMVGNRYLEKRLNLRVEHIKHSKC
RQEFLERVKANAAKRAEAKAQGVAVQLKRQPAQPRESRIVSTEGNVPQTL
APVPYETFI

Ligand information

>5obm Chain 1 (length=3100)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaggccagcaucag
uuuugguggcaggauaaauccauaggaauguagcuugccucgguaaguau
uauagccugugggaauacugccagcugggacugaggacugcgacguaagu
caaggaugcuggcauaaugguuauaugccgcccgucuugaaacacggacc
aaggagucuaacgucuaugcgaguguuuggguguaaaacccauacgcgua
augaaagugaacguagguuggggccucgcaagaggugcacaaucgaccga
uccugaugucuucggauggauuugaguaagagcauagcuguugggacccg
aaagauggugaacuaugccugaauagggugaagccagaggaaacucuggu
ggaggcucguagcgguucugacgugcaaaucgaucgucgaauuuggguau
aggggcgaaagacuaaucgaaccaucuaguagcugguuccugccgaaguu
ucccucaggauagcagaagcucguaucaguuuuaugagguaaagcgaaug
auuagagguuccggggucgaaaugaccuugaccuauucucaaacuuuaaa
uauguaagaaguccuuguuacuuaauugaacguggacauuugaaugaaga
gcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaugaac
cgaacguagaguuaaggugccggaauacacgcucaucagacaccacaaaa
gguguuaguucaucuagacagccggaaccggccgaaugaacuagcccuga
aaauggauggcgcucaagcguguuaccuauacucuaccgucaggguugau
augaugcccugacgaguaggcaggcguggaggucagugacgaagccuaga
ccguaaggucgggucgaacggccucuagugcagaucuuggugguaguagc
aaauauucaaaugagaacuuugaagacugaaguggggaaagguuccacgu
caacagcaguuggacguggguuagucgauccuaagagauggggaagcucc
guuucaaaggccugauuuuaugcaggccaccaucgaaagggaauccgguu
aagauuccggaaccuggauauggauucuucacgguaacguaacugaaugu
ggagacgucggcgcgagcccugggaggaguuaucuuuucuucuuaacagc
uuaucaccccggaauugguuuauccggagauggggucuuauggcuggaag
aggccagcaccuuugcuggcuccggugcgcuugugacggcccgugaaaau
ccacaggaaggaauaguuuucaugccaggucguacugauaaccgcagcag
gucuccaaggugaacagccucuaguugauagaauaauguagauaagggaa
gucggcaaaauagauccguaacuucgggauaaggauuggcucuaaggguc
gggacgaucaacuuagaacugguacggacaaggggaaucugacugucuaa
uuaaaacauagcauugcgauggucagaaagugauguugacgcaaugugau
uucugcccagugcucugaaugucaaagugaagaaauucaaccaagcgcgg
guaaacggcgggaguaacuaugacucucuuaagguagccaaaugccucgu
caucuaauuagugacgcgcaugaauggauuaacgagauucccacuguccc
uaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcagaauc
agcggggaaagaagacccuguugagcuugacucuaguuugacauugugaa
gagacaguuucuuuacuuauucaaugaagcggagcuggaauucauuuucc
acguucuagcauucaaggucccauucggggcugauccggguugaagacau
ugucagguggggaguuuggcuggggcggcacaucuguuaaacgauaacgc
agauguccuaaggggggcucauggagaacagaaaucuccaguagaacaaa
aggguaaaagcccccuugauuuugauuuucagugugaauacaaaccauga
aaguguggccuaucgauccuuuagucccucggaauuugaggcuagaggug
ccagaaaaguuaccacagggauaacuggcuuguggcagucaagcguucau
agcgacauugcuuuuugauucuucgaugucggcucuuccuaucauaccga
agcagaauucgguaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaau
guuaccgcaauaguaauugaacuuaguacgagaggaacaguucauucgga
uaauugguuuuugcggcugucugaucaggcauugccgcgaagcuaccauc
cgcuggauuauggcugaacgccucuaagucagaauccaugcuagaacgcg
gugauuucuuugcuccacacaauauagauggauacgaauaaggcguccuu
guggcgucgcugaaccauagcaggcuagcaacggugcacuuggcggaaag
gccuugggugcuugcuggcgaauugcaaugucauuuugcguggggauaaa
ucauuuguauacgacuuagauguacaacgggguauuguaagcaguagagu
agccuuguuguuacgaucugcugagauuaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5obm Aminoglycoside interactions and impacts on the eukaryotic ribosome.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): G2 K3 S4 H5 G6 Y7 R8 S9 R10 R12 Y13 M14 Q16 R17 F19 H22 G23 K35 D41 S47 Q49 K50 G51 H54 K55 Y57 Q58 G59 K60 T61 T68 K69 S70 S71 K78 V80 R83 K87 R88 N90 R92 K100 C101 E104 F105 R108 V109 K110 N112 R116 K120 V124 Q127 L128 K129 R130 P132
• Binding residue (residue number reindexed from 1): G1 K2 S3 H4 G5 Y6 R7 S8 R9 R11 Y12 M13 Q15 R16 F18 H21 G22 K34 D40 S46 Q48 K49 G50 H53 K54 Y56 Q57 G58 K59 T60 T67 K68 S69 S70 K77 V79 R82 K86 R87 N89 R91 K99 C100 E103 F104 R107 V108 K109 N111 R115 K119 V123 Q126 L127 K128 R129 P131

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

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:5obm, PDBe:5obm, PDBj:5obm
• PDBsum: 5obm
• PubMed: 29208708
• UniProt: Q02753|RL21A_YEAST Large ribosomal subunit protein eL21A (Gene Name=RPL21A)