Structure of PDB 6xiq Chain R Binding Site BS01

Receptor Information

>6xiq Chain R (length=188) Species: 4932 (Saccharomyces cerevisiae)

ANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIV
KKAVTVHSKSRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRV
LRRLLAKYRDAGKIDKHLYHVLYKESKGNAFKHKRALVEHIIQAKADAQR
EKALNEEAEARRLKNRAARDRRAQRVAEKRDALLKEDA

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): L4 R5 T6 K8 G18 K19 R20 K21 W23 R38 N39 K46 K53 T56 V57 H58 S59 K60 S61 R62 T63 R64 R74 H75 Y78 G79 K80 R81 K82 G83 T84 R85 A87 R88 L89 W95 I96 R100 R103 R110 D116 H118 Y120 H121 Y124 K125 K128 N130 I143 Q150
• Binding residue (residue number reindexed from 1): L3 R4 T5 K7 G17 K18 R19 K20 W22 R37 N38 K45 K52 T55 V56 H57 S58 K59 S60 R61 T62 R63 R73 H74 Y77 G78 K79 R80 K81 G82 T83 R84 A86 R87 L88 W94 I95 R99 R102 R109 D115 H117 Y119 H120 Y123 K124 K127 N129 I142 Q149

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: P0CX82|RL19A_YEAST Large ribosomal subunit protein eL19A (Gene Name=RPL19A)