Structure of PDB 6lqm Chain P Binding Site BS01

Receptor Information

>6lqm Chain P (length=50) Species: 9606 (Homo sapiens)

SSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL

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

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

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): S2 S3 H4 K5 K10 L13 Q17 K34 I35 R36 Y37 S39 K40 R41 R42 H43 W44 R45 K48 L49 L51
• Binding residue (residue number reindexed from 1): S1 S2 H3 K4 K9 L12 Q16 K33 I34 R35 Y36 S38 K39 R40 R41 H42 W43 R44 K47 L48 L50

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0002227 innate immune response in mucosa
• GO:0006412 translation
• GO:0019731 antibacterial humoral response
• GO:0050830 defense response to Gram-positive bacterium
• GO:0061844 antimicrobial humoral immune response mediated by antimicrobial peptide

Cellular Component

• GO:0005615 extracellular space
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6lqm, PDBe:6lqm, PDBj:6lqm
• PDBsum: 6lqm
• PubMed: 32669547
• UniProt: P62891|RL39_HUMAN Large ribosomal subunit protein eL39 (Gene Name=RPL39)