Structure of PDB 5lks Chain LY Binding Site BS01

Receptor Information

>5lks Chain LY (length=134) Species: 9606 (Homo sapiens)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>5lks Chain L5 (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: 5lks Structure-function insights reveal the human ribosome as a cancer target for antibiotics.
• Resolution: 3.6 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 P5 T8 S9 K13 R15 R17 K28 P33 R45 S46 R59 H61 K77 R87 N91 S102 K103 S125 R126
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 P5 T8 S9 K13 R15 R17 K28 P33 R45 S46 R59 H61 K77 R87 N91 S102 K103 S125 R126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5lks, PDBe:5lks, PDBj:5lks
• PDBsum: 5lks
• PubMed: 27665925
• UniProt: P61254|RL26_HUMAN Large ribosomal subunit protein uL24 (Gene Name=RPL26)