Structure of PDB 5lks Chain LT Binding Site BS01

Receptor Information

>5lks Chain LT (length=159) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEFMA

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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>>>>>>..<<<..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
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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): T2 N3 T4 K5 G6 K7 R8 R9 G10 R12 Y13 M14 F19 H22 K36 Q49 K50 G51 H54 K55 Y57 H58 K60 T61 T68 Q69 H70 A71 V80 K81 L85 K87 I89 R92 F105 R108 N112 D113 K116 W125 V126 L128 K129 R130 F140
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 G9 R11 Y12 M13 F18 H21 K35 Q48 K49 G50 H53 K54 Y56 H57 K59 T60 T67 Q68 H69 A70 V79 K80 L84 K86 I88 R91 F104 R107 N111 D112 K115 W124 V125 L127 K128 R129 F139

Gene Ontology

Molecular Function

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

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:5lks, PDBe:5lks, PDBj:5lks
• PDBsum: 5lks
• PubMed: 27665925
• UniProt: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)