Structure of PDB 4v6x Chain CD Binding Site BS01

Receptor Information

>4v6x Chain CD (length=289) Species: 9606 (Homo sapiens)

NKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNR
DIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARR
LLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNK
VFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMGQNVADYM
RYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENPVYEKKPK
KEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Ligand information

>4v6x Chain A5 (length=4298)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgccccccguuccucccgaccccuccacccgccc
ucccuucccccgccgccccgggcuccggcgggugcgggggugggcgggcg
gggccggggguggggucggcgggggaccgucccccgaccggcgaccggcc
gccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggga
cggcugggaaggcccggcggggaagguggcucggggggccccguccgucc
guccggcggcggcggcggcggcgggaccgaaaccccccccgaguguuaca
gcccccccggcagcagcacucgccgaaucccggggccgagggagcgagac
ccgucgccgcgcucuccccccucccggcgcccacccccgcggggacuccc
ccgcgggggcgcgccggcgucuccucgugggggggccgggccaccccucc
cacggcgcgaccgcucucccaccccuccuccccgcgcccccggggugccg
cgcgcgggucggggggcggggcggacuguccccagugcgccccgggcggg
ucgcgccgucgggcccgggggagguucucucggggccacgcgcgcguccc
ccgaagagggggacggcggagcgagcgcacggggucggcggcgacgucgg
cuacccacccgacccgucuugaaacacggaccaaggagucuaacacgugc
gcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaagg
ccggcgcgcucgccggccgaggugggaucccgaggccucuccaguccgcc
gagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagca
cgagcgcacguguuaggacccgaaagauggugaacuaugccugggcaggg
cgaagccagaggaaacucugguggagguccguagcgguccugacgugcaa
aucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucua
guagcugguucccuccgaaguuucccucaggauagcuggcgcucucgcag
acccgacgcacccccgccacgcaguuuuauccgguaaagcgaaugauuag
aggucuuggggccgaaacgaucucaaccuauucucaaacuuuaaaugggu
aagaagcccggcucgcuggcguggagccgggcguggaaugcgagugccua
gugggccacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgc
cggguuaaggcgcccgaugccgacgcucaucagaccccagaaaagguguu
gguugauauagacagcaggacgguggccauggaagucggaauccgcuaag
gaguguguaacaacucaccugccgaaucaacuagcccugaaaauggaugg
cgcuggagcgucgggcccauacccggccgucgccggcagucgagagugga
cgggagcggcgggggcggcgcgcgcgcgcgcgcguguggugugcgucgga
gggcggccuccucccgcccacgccccgcuccccgcccccggagccccgcg
gacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagcc
uagggcgcgggcccggguggagccgccgcaggugcagaucuuggugguag
uagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguucc
augugaacagcaguugaacaugggucagucgguccugagagaugggcgag
cgccguuccgaagggacgggcgauggccuccguugcccucggccgaucga
aagggagucggguucagauccccgaauccggaguggcggagaugggcgcc
gcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggga
gccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaau
ggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccg
gcggcguccggugagcucucgcuggcccuugaaaauccgggggagagggu
guaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggug
aacagccucuggcauguuggaacaauguagguaagggaagucggcaagcc
ggauccguaacuucgggauaaggauuggcucuaagggcugggucggucgg
gcuggggcgcgaagcggggcugggcgcgcgccgcggcuggaucuggacgc
gagccgggcccuucccguggaucgccccagcugcggcgggcgucgcggcc
gcgcgguuccgcgcggcgccucgccucggccggcgccuagcagccgacuu
agaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcau
cgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcu
cugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggag
uaacuaugacucucuuaagguagccaaaugccucgucaucuaauuaguga
cgcgcaugaauggaugaacgagauucccacugucccuaccuacuauccag
cgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaag
acccuguugagcuugacucuagucuggcacggugaagagacaugagaggu
guagaauaagugggaggcccccggcgcccccccgguguccccgcgagggg
cccggggcgggguccgccggcccugcgggccgccggugaaauaccacuac
ucugaucguuuuuucacugacccggugaggcgggggggcgagccccgagg
ggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcga
cccgcuccggggacagugccagguggggaguuugacuggggcgguacacc
ugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaa
ccucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagua
cgaauacagaccgugaaagcggggccucacgauccuucugaccuuuuggg
uuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugug
gcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcu
cuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugauguguuguugccaugguaauccugcucaguacgaga
ggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaau
ggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucaga
aucccgcccaggcggaacgauacggcagcgccgcggagccucgguuggcc
ucggauagccggucccccgccuguccccgccggcgggccgcccccccccu
ccacgggagggcgcgugccccgccgcgcgccgggaccgggguccggugcg
gagugcccuucguccugggaaacggggcgcggccggagaggcggccgccc
ccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaaccau
ucguagacgaccugcuucugggucgggguuucguacguagcagagcagcu
cccucgcugcgaucuauugaaagucagcccucgacacaaggguuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4v6x Structures of the human and Drosophila 80S ribosome.
• Resolution: 5.0 Å
• Binding residue (original residue number in PDB): Y12 R15 Y16 Q17 K19 R23 T28 R35 K43 Y44 T46 K48 F113 G140 A141 T143 Y145 A148 L150 T153 F160 P174 S176 K178 R179 R268 D278 Q282 R289
• Binding residue (residue number reindexed from 1): Y4 R7 Y8 Q9 K11 R15 T20 R27 K35 Y36 T38 K40 F105 G132 A133 T135 Y137 A140 L142 T145 F152 P166 S168 K170 R171 R260 D270 Q274 R281

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0008097 5S rRNA binding
• GO:0019843 rRNA binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0048027 mRNA 5'-UTR binding
• GO:1990948 ubiquitin ligase inhibitor activity

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1904667 negative regulation of ubiquitin protein ligase activity
• GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
• GO:2000435 negative regulation of protein neddylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0032991 protein-containing complex
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:4v6x, PDBe:4v6x, PDBj:4v6x
• PDBsum: 4v6x
• PubMed: 23636399
• UniProt: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)