Structure of PDB 6xiq Chain L Binding Site BS01

Receptor Information

>6xiq Chain L (length=193) Species: 4932 (Saccharomyces cerevisiae)

AISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPL
DLLRPVVRAPTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRR
QNRNQEIFDANVQRLKEYQSKIIVFPRNGKAPEAEQVLSAAATFPIAQPA
TDVEARAVQDNGESAFRTLRLARSEKKFRGIREKRAREKAEAE

Ligand information

>6xiq Chain 1 (length=3223)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggauuaacg
agauucccacugucccuaucuacuaucuagcgaaaccacagccaagggaa
cgggcuuggcagaaucagcggggaaagaagacccuguugagcuugacucu
aguuugacauugugaagagacauagaggguguagaauaagugggagcuuc
ggcgccagugaaauaccacuaccuuuauaguuucuuuacuuauucaauga
agcggagcuggaauucauuuuccacguucuagcauucaaggucccauucg
gggcugauccggguugaagacauugucagguggggaguuuggcuggggcg
gcacaucuguuaaacgauaacgcagauguccuaaggggggcucauggaga
acagaaaucuccaguagaacaaaaggguaaaagcccccuugauuuugauu
uucagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucc
cucggaauuugaggcuagaggugccagaaaaguuaccacagggauaacug
gcuuguggcagucaagcguucauagcgacauugcuuuuugauucuucgau
gucggcucuuccuaucauaccgaagcagaauucgguaagcguuggauugu
ucacccacuaauagggaacgugagcuggguuuagaccgucgugagacagg
uuaguuuuacccuacugaugaauguuaccgcaauaguaauugaacuuagu
acgagaggaacaguucauucggauaauugguuuuugcggcugucugauca
ggcauugccgcgaagcuaccauccgcuggauuauggcugaacgccucuaa
gucagaauccaugcuagaacgcggugauuucuuugcuccacacaauauag
auggauacgaauaaggcguccuuguggcgucgcugaaccauagcaggcua
gcaacggugcacuuggcggaaaggccuugggugcuugcuggcgaauugca
augucauuuugcguggggauaaaucauuuguauacgacuuagauguacaa
cgggguauuguaagcaguagaguagccuuguuguuacgaucugcugagau
uaagccuuuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xiq Structural impact of K63 ubiquitin on yeast translocating ribosomes under oxidative stress.
• Resolution: 4.2 Å
• Binding residue (original residue number in PDB): S4 N12 H13 F14 R15 K16 H17 W18 E20 Q28 K32 R35 R36 R39 D52 L53 R55 R59 P61 T62 Y65 N66 K68 R70 R73 R91 H99 R100 R101 Q102 R104 R128 R171 R174 K178 R183 K185
• Binding residue (residue number reindexed from 1): S3 N11 H12 F13 R14 K15 H16 W17 E19 Q27 K31 R34 R35 R38 D51 L52 R54 R58 P60 T61 Y64 N65 K67 R69 R72 R90 H98 R99 R100 Q101 R103 R127 R170 R173 K177 R182 K184

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• 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:6xiq, PDBe:6xiq, PDBj:6xiq
• PDBsum: 6xiq
• PubMed: 32855298
• UniProt: Q12690|RL13A_YEAST Large ribosomal subunit protein eL13A (Gene Name=RPL13A)