Structure of PDB 6xiq Chain X Binding Site BS01

Receptor Information

>6xiq Chain X (length=121) Species: 4932 (Saccharomyces cerevisiae)

KALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSYKVIEQPITSET
AMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTKK
AYVRLTADYDALDIANRIGYI

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

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): T31 F32 R33 L34 K39 L40 R42 A43 K45 Y46 S69 K92 Y93 K109 T112 L113 V114 Y123 R125
• Binding residue (residue number reindexed from 1): T10 F11 R12 L13 K18 L19 R21 A22 K24 Y25 S48 K71 Y72 K88 T91 L92 V93 Y102 R104

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0019843 rRNA binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• 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:0030687 preribosome, large subunit precursor
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xiq, PDBe:6xiq, PDBj:6xiq
• PDBsum: 6xiq
• PubMed: 32855298
• UniProt: P04456|RL25_YEAST Large ribosomal subunit protein uL23 (Gene Name=RPL25)