Structure of PDB 6lqm Chain O Binding Site BS01

Receptor Information

>6lqm Chain O (length=69) Species: 9606 (Homo sapiens)

PRKIEEIKDFLLTARRKDAKSVKIKKNKDNVKFKVRCSRYLYTLVITDKE
KAEKLKQSLPPGLAVKELK

Ligand information

>6lqm Chain 2 (length=3532)

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
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucgagaguggacgggagcggcggcccggagccccgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaaua
uucaaacgagaacuuugaaggccgaaguggagaaggguuccaugugaaca
gcaguugaacaugggucagucgguccugagagaugggcgagcgccguucc
gaagggacgggcgauggccuccguugcccucggccgaucgaaagggaguc
ggguucagauccccgaauccggaguggcggagaugggcgccgcgaggcgu
ccagugcgguaacgcgaccgaucccggagaagccggcgggagccccgggg
agaguucucuuuucuuugugaagggcagggcgcccuggaauggguucgcc
ccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcgucc
ggugagcucucgcuggcccuugaaaauccgggggagaggguguaaaucuc
gcgccgggccguacccauauccgcagcaggucuccaaggugaacagccuc
uggcauguuggaacaauguagguaagggaagucggcaagccggauccgua
acuucgggauaaggauuggcucuaagggcuggagccgacuuagaacuggu
gcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggc
ccgcggcggguguugacgcgaugugauuucugcccagugcucugaauguc
aaagugaagaaauucaaugaagcgcggguaaacggcgguuaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuc
ccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcu
uggcggaaucagcggggaaagaagacccuguugagcuugacucuagucug
gcacggugaaguuuucacugacccggugaggcgggggggcgagccccgag
gggcucucgcuucuggcgccaagcgcccggccgcgcgccggccgggcgcg
acccgcuccggggacagugccagguggggaguuugacuggggcgguacac
cugucaaacgguaacgcagguguccuaaggcgagcucagggaggacagaa
accucccguggagcagaagggcaaaagcucgcuugaucuugauuuucagu
acgaauacagaccgugaaagcggggccucacgauccuucugaccuuuugg
guuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcuugu
ggcggccaagcguucauagcgacgucgcuuuuugauccuucgaugucggc
ucuuccuaucauugugaagcagaauucaccaagcguuggauuguucaccc
acuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguu
uuacccuacugaugauguguuguugccaugguaauccugcucaguacgag
aggaaccgcagguucagacauuugguguaugugcuuggcugaggagccaa
uggggcgaagcuaccaucugugggauuaugacugaacgccucuaagucag
aaucccgcccaggcggaacgauacggcagcgccgcggagccucgguuggc
cucggauagccggucccccgccgggguccggugcggagugcccuucgucc
ugggaaacggggcgcggccggagaggcggccgcccccucgcccgucacgc
accgcacguucguggggaaccuggcgcuaaaccauucguagacgaccugc
uucugggucgggguuucguacguagcagagcagcucccucgcugcgaucu
auugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6lqm Structural snapshots of human pre-60S ribosomal particles before and after nuclear export.
• Resolution: 3.09 Å
• Binding residue (original residue number in PDB): P2 R3 K4 D19 K24 K26 K33 K35 R37 S39 R40 Y41 L42 T44 L69
• Binding residue (residue number reindexed from 1): P1 R2 K3 D18 K23 K25 K32 K34 R36 S38 R39 Y40 L41 T43 L68

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0001501 skeletal system development
• GO:0001503 ossification
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0007605 sensory perception of sound
• GO:0022618 protein-RNA complex assembly
• GO:0034463 90S preribosome assembly
• GO:0042474 middle ear morphogenesis
• GO:0048318 axial mesoderm development

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0033291 eukaryotic 80S initiation complex
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqm, PDBe:6lqm, PDBj:6lqm
• PDBsum: 6lqm
• PubMed: 32669547
• UniProt: P63173|RL38_HUMAN Large ribosomal subunit protein eL38 (Gene Name=RPL38)