Structure of PDB 5t2c Chain q Binding Site BS02

Receptor Information

>5t2c Chain q (length=176) Species: 9606 (Homo sapiens)

QDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSK
ARYTVRSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDT
GNFGFGIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIG
AKHRISKEEAMRWFQQKYDGIILPGK

Ligand information

>5t2c Chain A (length=3776)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucggccgaguguuacagcc
cccccggcagcagcacucgccgaaucccggggccgagggagcgagacccg
ucgccgcgcucuccccccucccggcgccgccggggggggccgggccaccc
cucccacggcgcgaccgcucggggcggacuguccccagugcgccccgggc
gggucgcgccgucgggcccgggggaggggccacgcgcgcgucccccgaag
agggggacggcggagcgagcgcacggggucggcggcgacgucggcuaccc
acccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgagu
cgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcg
cgcucgccggccgaggugggaucccgaggccucuccaguccgccgagggc
gcaccaccggcccgucucgcccgccgcgccggggagguggagcacgagcg
cacguguuaggacccgaaagauggugaacuaugccugggcagggcgaagc
cagaggaaacucugguggagguccguagcgguccugacgugcaaaucggu
cguccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcu
gguucccuccgaaguuucccucaggauagcuggcgcucucgcacacgcag
uuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucuc
aaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguga
gccgggcguggaauggagugccuagugggccacuuuugguaagcagaacu
ggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgc
ucaucagaccccagaaaagguguugguugauauagacagcaggacggugg
ccauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagcggcgggggcggcgcgcgcg
cgcgcccgcccccggagccccgcggacgcuacgccgcgacgaguaggagg
gccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgc
cgcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuug
aaggccgaaguggagaaggguuccaugugaacagcaguugaacauggguc
agucgguccugagagaugggcgagcgccguuccgaagggacgggcgaugg
ccuccguugcccucggccgaucgaaagggagucggguucagauccccgaa
uccggaguggcggagaugggcgccgcgaggcguccagugcgguaacgcga
ccgaucccggagaagccggcgggagccccggggagaguucucuuuucuuu
gugaagggcagggcgcccuggaauggguucgccccgagagaggggcccgu
gccuuggaaagcgucgcgguuccggcggcguccggugagcucucgcuggc
ccuugaaaauccgggggagaggguguaaaucucgcgccgggccguaccca
uauccgcagcaggucuccaaggugaacagccucuggcauguuggaacaau
guagguaagggaagucggcaagccggauccguaacuucgggauaaggauu
ggcucuaagggcugggucggucgucggccggcgccuagcagccgacuuag
aacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucg
cgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcucu
gaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagua
acuaugacucucuuaagguagccaaaugccucgucaucuaauuagugacg
cgcaugaauggaugaacgagauucccacugucccuaccuacuauccagcg
aaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaagac
ccuguugagcuugacucuagucuggcacggugaagagacaugagaggugu
agaauaagugggaggcccccggcgcccccccgguguccccgcgaggggcc
cggggcgggguccgccggcccugcgggccgccggugaaauaccacuacuc
ugaucguuuuuucacugacccggugaggcgggggggcgagccccgagggg
cucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcgacc
cgcuccggggacagugccagguggggaguuugacuggggcgguacaccug
ucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaaacc
ucccguggagcagaagggcaaaagcucgcuugaucuugauuuucaguacg
aauacagaccgugaaagcggggccucacgauccuucugaccuuuuggguu
uuaagcaggaggugucagaaaaguuaccacagggauaacuggcuuguggc
ggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggcucu
uccuaucauugugaagcagaauucaccaagcguuggauuguucacccacu
aauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuua
cccuacugaugauguguuguugccaugguaauccugcucaguacgagagg
aaccgcagguucagacauuugguguaugugcuuggcugaggagccaaugg
ggcgaagcuaccaucugugggauuaugacugaacgccucuaagucagaau
cccgcccaggcggaacgauacggcagcgccgcggagccucgguuggccuc
ggauagccggucccccgcgggguccggugcggagugcccuucguccuggg
aaacggggcgcggccggagaggcggccgcccccucgcccgucacgcacgc
cguucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugg
gucgggguuucguacguagcagagcagcucccucgcugcgaucuauugaa
agucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5t2c Structures and stabilization of kinetoplastid-specific split rRNAs revealed by comparing leishmanial and human ribosomes.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): K19 N23 C25 A53 R54 F60 N98 S100 D101 G106 F107 G127 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K17 N21 C23 A51 R52 F58 N96 S98 D99 G104 F105 G125 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:5t2c, PDBe:5t2c, PDBj:5t2c
• PDBsum: 5t2c
• PubMed: 27752045
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)