Structure of PDB 6z6m Chain LJ Binding Site BS01

Receptor Information

>6z6m Chain LJ (length=176) Species: 9606 (Homo sapiens)

QDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSK
ARYTVRSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDT
GNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIG
AKHRISKEEAMRWFQQKYDGIILPGK

Ligand information

>6z6m Chain L5 (length=3772)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggccggagccccgcggacgcuacgccgcgacgaguaggagggccgcu
gcggugagccuugaagccuagggcgcgggcccggguggagccgccgcagg
ugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggcc
gaaguggagaaggguuccaugugaacagcaguugaacaugggucagucgg
uccugagagaugggcgagcgccguuccgaagggacgggcgauggccuccg
uugcccucggccgaucgaaagggagucggguucagauccccgaauccgga
guggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgauc
ccggagaagccggcgggagccccggggagaguucucuuuucuuugugaag
ggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuug
gaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuuga
aaauccgggggagaggguguaaaucucgcgccgggccguacccauauccg
cagcaggucuccaaggugaacagccucuggcauguuggaacaauguaggu
aagggaagucggcaagccggauccguaacuucgggauaaggauuggcucu
aagggcugggucggucgcggccggcgccuagcagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuauga
cucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcauga
auggaugaacgagauucccacugucccuaccuacuauccagcgaaaccac
agccaagggaacgggcuuggcggaaucagcggggaaagaagacccuguug
agcuugacucuagucuggcacggugaagagacaugagagguguagaauaa
gugggaggcccccggcgcccccccgguguccccgcgaggggcccggggcg
ggguccgccggcccugcgggccgccggugaaauaccacuacucugaucgu
uuuuucacugacccggugaggcgggggggcgagccccgaggggcucucgc
uucuggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccg
gggacagugccagguggggaguuugacuggggcgguacaccugucaaacg
guaacgcagguguccuaaggcgagcucagggaggacagaaaccucccgug
gagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacag
accgugaaagcggggccucacgauccuucugaccuuuuggguuuuaagca
ggaggugucagaaaaguuaccacagggauaacuggcuuguggcggccaag
cguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuauc
auugugaagcagaauucaccaagcguuggauuguucacccacuaauaggg
aacgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacu
gaugauguguuguugccaugguaauccugcucaguacgagaggaaccgca
gguucagacauuugguguaugugcuuggcugaggagccaauggggcgaag
cuaccaucugugggauuaugacugaacgccucuaagucagaaucccgccc
aggcggaacgauacggcagcgccgcggagccucgguuggccucggauagc
cggucccccgccgggguccggugcggagugcccuucguccugggaaacgg
ggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacguu
cguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaaguc
agcccucgacacaaggguuugu

.........................<<<<<<.....<......>......
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..>>>>>..<<<<<<<<<<...<<<<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>>>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....<<<<<..((((((>>>>>..>>>..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
....<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<...<...<<
....<<<<.<<<..<<......>>>>>>>>>>>...>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
.<<<<...<<..<<<.<<.<<<<......<<<<<<<<..>>>>>>>>...
....>>>>.>>>>>........>>>>>>...>>>>>>>>>>.........
...........<<<<<<.<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<<.<<<<..<<<<..<...........>...>>>
>..>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<<.
....>>>>>>>>.>>....>>>>>>.....>>>.>>>>>....>>>>...
>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<.
.<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<
<<......>>>>>>>..<<<<<...<<<..<<<..((((.((((>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<<.<<.<<........>>
>>>>>>....>>>>>>>>>...<<.......>>......>>>>>>.....
.>.>>..<<<<<<....<.<<<....>>>.><<.<<<<<<<.........
.............<<<.<<<<<<<<<...<<<....<<<..<.<<<..<.
.................>.>>>.>..>>>..>.>>...>>>>>>>...<<
<<<<<<<.........>>>>>>>>>....>>>>>>>>>>>>..>>..<<<
<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<..
.<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<<
.......<<<<<.<<<...<<.........>>...>>>.........<<.
.....>>...>>>>>...>>>>>>>>>>>>>..........))).>>...
>>>>>..>>>...>>>>>>><<<<<<.<<<..........)))).)))).
..<....>..................>>>>>>>>>....>>>>>>.<.<<
<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>>.
.>.....>>>>>><<.....<<.....<<<<<<.......>>>>>>.<<<
.....<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<
<<<...<<....<<<....>>>..........<<.<<<<<.<.<....>>
.>>>>>>>......>>....>>>..<<<<<........>>>>>))<<<<.
...<<<<<..<<<<<<<<....>>>>>>>>..<<<....>>>...<..<<
<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<
<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>>.
....<<<<<<<.......>>>>>>>>>>>...>>>>>>>>>>>>......
...>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<<.
.....>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<<<
<.<<.........<.....<<<<<....<<..>>.....>>>>><<.<<<
<<<<<<<<..<<..........>>.......>>>>>..>>>>>>.>>...
.........<<<<<<<<<..<<<.........>>>..<<<<<<<....<<
<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<....<<<.
....<<<<....>>>>.....>>>.>>>>..>>>>><<<<<<.......>
>>>>>........<...........<<<<<.......>>>>>.....>..
...>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>..
..<<<<<........>>>>>....<<<<<..<<<.<<......<<<<.<<
<<<<..<<<<<.<<<<<<<<<.<<<<<<<<....................
..................................................
..<....>..........................................
>>>>>>>>...<<<<<.....<<<<........<........>.......
............<<<<<<<<<<.......>>>>>>>>>>..>>>>..>>>
>>....>>>>>>>>>..>>>>>...<<<.....>>>..<<<<<<......
.....>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>...
..<<.[.(((>>....>>>>>>>...<<<..<<<<.......>>>>..>>
><<<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>
>>>>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<
<.......>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<
.<.<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>
>..>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>
>>>.....<<<<<<.<..<<<....<<<<<.................>>>
>>..<<<<....<<<<....<<.<<<<<<<]]].>>>>>..>>.>>...>
>>>...>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>
>...>.>>>>>>.....<<<<<<<.<<..<<<<....<<<........<<
<<<.<<<<....>>>>.>>>>>.......>>>...<<<..<<<<....<<
<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>...........
...>>>>..>>>>>>>>><<<<<.<.............>....<<.<<<<
<<<.<<.....<<<<....<<<<<......>>>>>...>>>>....>>..
..>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6z6m Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 S51 A53 S59 F60 N97 N98 S100 D101 T102 G106 F107 G108 G127 L128 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K17 C19 N21 C23 S49 A51 S57 F58 N95 N96 S98 D99 T100 G104 F105 G106 G125 L126 D127 Y129 K143

Gene Ontology

Molecular Function

• GO:0003723 RNA 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: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:0006605 protein targeting
• GO:0010628 positive regulation of gene expression
• GO:0032092 positive regulation of protein binding
• GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
• GO:0034504 protein localization to nucleus
• GO:0042273 ribosomal large subunit biogenesis
• GO:0050821 protein stabilization
• GO:1901796 regulation of signal transduction by p53 class mediator
• GO:1901798 positive 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:0005829 cytosol
• GO:0005840 ribosome
• 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:6z6m, PDBe:6z6m, PDBj:6z6m
• PDBsum: 6z6m
• PubMed: 32687489
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)