Structure of PDB 5obm Chain m1 Binding Site BS01

Receptor Information

>5obm Chain m1 (length=169) Species: 559292 (Saccharomyces cerevisiae S288C)

QNPMRDLKIEKLVLNISVGESGDRLTRASKVLEQLSGQTPVQSKARYTVR
TFGIRRNEKIAVHVTVRGPKAEEILERGLKVKEYQLRDRNFSATGNFGFG
IDEHIDLGIKYDPSIGIFGMDFYVVMNRPGARVTRRKRCKGTVGNSHKTT
KEDTVSWFKQKYDADVLDK

Ligand information

>5obm Chain 5 (length=3134)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacauggcugggccag
caucaguuuugguggcaggauaaauccauaggaauguagcuugccucggu
aaguauuauagccugugggaauacugccagcugggacugaggacugcgac
guaagucaaggaugcuggcauaaugguuauaugccgcccgucuugaaaca
cggaccaaggagucuaacgucuaugcgaguguuuggguguaaaacccaua
cgcguaaugaaagugaacguagguuggggccucgcaagaggugcacaauc
gaccgauccugaugucuucggauggauuugaguaagagcauagcuguugg
gacccgaaagauggugaacuaugccugaauagggugaagccagaggaaac
ucugguggaggcucguagcgguucugacgugcaaaucgaucgucgaauuu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguuccugcc
gaaguuucccucaggauagcagaagcucguaucaguuuuaugagguaaag
cgaaugauuagagguuccggggucgagaccuugaccuauucucaaacuuu
aaauauguaagaaguccuuguuacuuaauugaacguggacauuugaauga
agagcuuuuagugggccauuuuugguaagcagaacuggcgaugcgggaug
aaccgaacguagaguuaaggugccggaauacacgcucaucagacaccaca
aaagguguuaguucaucuagacagccggacgguggccauggaagucggaa
uccgcuaaggaguguguaacaacucaccggccgaaugaacuagcccugaa
aauggauggcgcucaagcguguuaccuauacucuaccgucaggguuggau
gcccugacgaguaggcaggcguggaggucagugacgaagccuagaccgua
aggucgggucgaacggccucuagugcagaucuuggugguaguagcaaaua
uucaaaugagaacuuugaagacugaaguggggaaagguuccacgucaaca
gcaguuggacguggguuagucgauccuaagagauggggaagcuccguuuc
aaaggccucaggccaccaucgaaagggaauccgguuaagauuccggaacc
uggauauggauucuucacgguaacguaacugaauguggagacgucggcgc
gagcccugggaggaguuaucuuuucuucuuaacagcuuaucaccccggaa
uugguuuauccggagauggggucuuauggcuggaagaggccagcaccuuu
gcuggcuccggugcgcuugugacggcccgugaaaauccacaggaaggaau
aguuuucaugccaggucguacugauaaccgcagcaggucuccaaggugaa
cagccucuaguugauagaauaauguagauaagggaagucggcaaaauaga
uccguaacuucgggauaaggauuggcucuaagggucggacgaucaacuua
gaacugguacggacaaggggaaucugacugucuaauuaaaacauagcauu
gcgauggucagaaagugauguugacgcaaugugauuucugcccagugcuc
ugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcgggagu
aacuaugacucucuuaagguagccaaaugccucgucaucuaauuagugac
gcgcaugaauggauuaacgagauucccacugucccuaucuacuaucuagc
gaaaccacagccaagggaacgggcuuggcagaaucagcggggaaagaaga
cccuguugagcuugacucuaguuugacauugugaagagacguuucuuuac
uuauucaaugaagcggagcuggaauucauuuuccacguucuagcauucaa
ggucccauucggggcugauccggguugaagacauugucagguggggaguu
uggcuggggcggcacaucuguuaaacgauaacgcagauguccuaaggggg
gcucauggagaacagaaaucuccaguagaacaaaaggguaaaagcccccu
ugauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucga
uccuuuagucccucggaauuugaggcuagaggugccagaaaaguuaccac
agggauaacuggcuuguggcagucaagcguucauagcgacauugcuuuuu
gauucuucgaugucggcucuuccuaucauaccgaagcagaauucgguaag
cguuggauuguucacccacuaauagggaacgugagcuggguuuagaccgu
cgugagacagguuaguuuuacccuacugaugaauguuaccgcaauaguaa
uugaacuuaguacgagaggaacaguucauucggauaauugguuuuugcgg
cugucugaucaggcauugccgcgaagcuaccauccgcuggauuauggcug
aacgccucuaagucagaauccaugcuagaacgcggugauuucuuugcucc
acacaauauagauggauacgaauaaggcguccuuguggcgucgcugaacc
auagcaggcuagcaacggugcacuuggcggaaaggccuugggugcuugcu
ggcgaauugcaaugucauuuugcguggggauaaaucauuuguauacgacu
uagauguacaacgggguauuguaagcaguagaguagccuuguuguuacga
ucugcugagauuaagccuuuguugucugauuugu

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

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): K16 V18 N20 S22 G24 S48 A50 R51 Y52 V54 T56 F57 I59 H68 R94 N95 S97 A98 T99 N101 G103 F104 G105 G124 M125 D126 Y128 K142
• Binding residue (residue number reindexed from 1): K11 V13 N15 S17 G19 S43 A45 R46 Y47 V49 T51 F52 I54 H63 R89 N90 S92 A93 T94 N96 G98 F99 G100 G119 M120 D121 Y123 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:5obm, PDBe:5obm, PDBj:5obm
• PDBsum: 5obm
• PubMed: 29208708
• UniProt: Q3E757|RL11B_YEAST Large ribosomal subunit protein uL5B (Gene Name=RPL11B)