Structure of PDB 5lks Chain Lh Binding Site BS01

Receptor Information

>5lks Chain Lh (length=122) Species: 9606 (Homo sapiens)

AKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVR
KSIARVLTVINQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEEN
LKTKKQQRKERLYPLRKYAVKA

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

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

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): Y73 K74 G75 K77 R89 R94 N96 K97 H98 K106 R109 E111 R112
• Binding residue (residue number reindexed from 1): Y72 K73 G74 K76 R88 R93 N95 K96 H97 K105 R108 E110 R111

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• 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:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5lks, PDBe:5lks, PDBj:5lks
• PDBsum: 5lks
• PubMed: 27665925
• UniProt: P42766|RL35_HUMAN Large ribosomal subunit protein uL29 (Gene Name=RPL35)