Structure of PDB 6olz Chain AJ Binding Site BS02

Receptor Information

>6olz Chain AJ (length=169) Species: 9606 (Homo sapiens)

ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVR
SFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFG
IQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRIS
KEEAMRWFQQKYDGIILPG

Ligand information

>6olz Chain A2 (length=3643)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggaagc
gagacgucgccgcgcucuccccccugggggggccgggccaccccucccac
ggcgcgaccgcucucccagggggcggggcggacuguccccagugcgcccc
gggcgggucgcgccgucgggcccggggggccacgcgcgcgucccgggacg
gcggagcgagcgcacggggucggcggcgacgucggcuacccacccgaccc
gucuugaaacacggaccaaggagucuaacacgugcgcgagucgggggcuc
gcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccg
gccgaggugggaucccgaggccucuccaguccgccgaggggcaccaccgg
cccgucucgcccgccgcgccggggagguggagcacgagcgcacguguuag
gacccgaaagauggugaacuaugccugggcagggcgaagccagaggaaac
ucugguggagguccguagcgguccugacgugcaaaucggucguccgaccu
ggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucccucc
gaaguuucccucaggauagcuggcgcucucgcccacgcaguuuuauccgg
uaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccuauucu
caaacuuuaaauggguaagaagcccggcucgcuggcguggagccggggug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcgucgagaguggacgggagcggcggcccgcccgcggacgcuacgccgcg
acgaguaggagggccgcugcggugagccuugaagccuagggcgcgggccc
ggguggagccgccgcaggugcagaucuuggugguaguagcaaauauucaa
acgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcagu
ugaacaugggucagucgguccugagagaugggcgagcgccguuccgaagg
gacgggcgauggccuccguugcccucggccgaucgaaagggagucggguu
cagauccccgaauccggaguggcggagaugggcgccgcgaggcguccagu
gcgguaacgcgaccgaucccggagaagccggcgggagccccggggagagu
ucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgag
agaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgguga
gcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgcc
gggccguacccauauccgcagcaggucuccaaggugaacagccucuggca
uguuggaacaauguagguaagggaagucggcaagccggauccguaacuuc
gggauaaggauuggcucuaagggcuggcagccgacuuagaacuggugcgg
accaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgc
ggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaag
ugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacucu
cuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaugg
augaacgagauucccacugucccuaccuacuauccagcgaaaccacagcc
aagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcu
ugacucuagucuggcacggugaagagacaugauagaauaagugggaggcc
cgggccgccggugaaauaccacuacucugaucguuuuuucacugacccgg
ugaggcgggggggcgagcccgaggggcucucgcuucuggcgccaagcgcc
cgcccggccgggcgcgacccgcuccggggacagugccagguggggaguuu
gacuggggcgguacaccugucaaacgguaacgcagguguccuaaggcgag
cucagggaggacagaaaccucccguggagcagaagggcaaaagcucgcuu
gaucuugauuuucaguacgaauacagaccgugaaagcggggccucacgau
ccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuaccaca
gggauaacuggcuuguggcggccaagcguucauagcgacgucgcuuuuug
auccuucgaugucggcucuuccuaucauugugaagcagaauucgccaagc
guuggauuguucacccacuaauagggaacgugagcuggguuuagaccguc
gugagacagguuaguuuuacccuacugaugauguguuguugccaugguaa
uccugcucaguacgagaggaaccgcagguucagacauuugguguaugugc
uuggcugaggagccaauggggcgaagcuaccaucugugggauuaugacug
aacgccucuaagucagaaucccgcccaggcggaacgauacggcagcgccg
cggagccucgguuggccucggauagccgguccgggguccggugcggagug
cccuucguccugggaaacggggcgcggccggaaaggcggccgcccccucg
cccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucgua
gacgaccugcuucugggucgggguuucguacguagcagagcagcucccuc
gcugcgaucuauugaaagucagcccucgacacaaggguuuguc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6olz Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 S51 A53 F60 N98 D101 T102 N104 F107 G127 L128 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K11 C13 N15 C17 S43 A45 F52 N90 D93 T94 N96 F99 G119 L120 D121 Y123 K137

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:6olz, PDBe:6olz, PDBj:6olz
• PDBsum: 6olz
• PubMed: 31160784
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)