Structure of PDB 6om0 Chain U Binding Site BS02

Receptor Information

>6om0 Chain U (length=157) Species: 9606 (Homo sapiens)

TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKG
MPHKCYHGKTGRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKS
RDSFLKRVKENDQKKKEAKEKGTWVQLKRQPAPPREAHFVRTNGKEPELL
EPIPYEF

Ligand information

>6om0 Chain t (length=3607)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgcccccggggucggcgggggaccgucccccggaccggcg
accggccgccgccgggcgcauuuccaggcggugcgccgcgaccggcuccg
ggacggcugggaaggcccggcggggaagguggcucggggcccccgagugu
uacagcccccccggcagcagcacucgccgaaucccggggccgagggagcg
agacccgucgccgcgcucuccccccugggggggccgggccaccccuccca
cggcgcgaccgcucucccagggggcggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccggggggccacgcgcgcgucccccgaa
gggggggacggcggagagcgcacggggucggcggcgacgucggcuaccca
cccgacccgucuugaaacacggaccaaggagucuaacacgugcgcgaguc
gggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgc
gcucgccggccgaggugggaucccgaggccucuccaguccgccgaggggc
accaccggcccgucucgcccgccgcgccggggagguggagcacgagcgca
cguguuaggacccgaaagauggugaacuaugccugggcagggcgaagcca
gaggaaacucugguggagguccguagcgguccugacgugcaaaucggucg
uccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugg
uucccuccgaaguuucccucaggauagcuggcgcucucgcccacgcaguu
uuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaa
ccuauucucaaacuuuaaauggguaagaagcccggcucgcuggcguggag
ccgggguggaaugcgagugccuagugggccacuuuugguaagcagaacug
gcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcu
caucagaccccagaaaagguguugguugauauagacagcaggacgguggc
cauggaagucggaauccgcuaaggaguguguaacaacucaccugccgaau
caacuagcccugaaaauggauggcgcuggagcgucgggcccauacccggc
cgucgccggcgucgagaguggacgggagcggcggcccggagccccgcgga
cgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagccua
gggcgcgggcccggguggagccgccgcaggugcagaucuuggugguagua
gcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuccau
gugaacagcaguugaacaugggucagucgguccugagagaugggcgagcg
ccguuccgaagggacgggcgauggccuccguugcccucggccgaucgaaa
gggagucggguucagauccccgaauccggaguggcggagaugggcgccgc
gaggcguccagugcgguaacgcgaccgaucccggagaagccggcgggagc
cccggggagaguucucuuuucuuugugaagggcagggcgcccuggaaugg
guucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggc
ggcguccggugagcucucgcuggcccuugaaaauccgggggagagggugu
aaaucucgcgccgggccguacccauauccgcagcaggucuccaaggugaa
cagccucuggcauguuggaacaauguagguaagggaagucggcaagccgg
auccguaacuucgggauaaggauuggcucuaagggcuggcagccgacuua
gaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcauc
gcgaaggcccgcggcggguguugacgcgaugugauuucugcccagugcuc
ugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgggagu
aacuaugacucucuuaagguagccaaaugccucgucaucuaauuagugac
gcgcaugaauggaugaacgagauucccacugucccuaccuacuauccagc
gaaaccacagccaagggaacgggcuuggcggaaucagcggggaaagaaga
cccuguugagcuugacucuagucuggcacggugaagagacguuuuuucac
ugacccggugaggcgggggggcgagcccgaggggcucucgcuucuggcgc
caagcgcccgcccggccgggcgcgacccgcuccggggacagugccaggug
gggaguuugacuggggcgguacaccugucaaacgguaacgcagguguccu
aaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaaa
gcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggc
cucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaag
uuaccacagggauaacuggcuuguggcggccaagcguucauagcgacguc
gcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaauu
cgccaagcguuggauuguucacccacuaauagggaacgugagcuggguuu
agaccgucgugagacagguuaguuuuacccuacugaugauguguuguugc
caugguaauccugcucaguacgagaggaaccgcagguucagacauuuggu
guaugugcuuggcugaggagccaauggggcgaagcuaccaucugugggau
uaugacugaacgccucuaagucagaaucccgcccaggcggaacgauacgg
cagcgccgcggagccucgguuggccucggauagccgguccccgccggggg
uccggugcggagugcccuucguccugggaaacggggcgcggccggaaagg
cggccgcccccucgcccgucacgcaccgcacguucguggggaaccuggcg
cuaaaccauucguagacgaccugcuucugggucgggguuucguacguagc
agagcagcucccucgcugcgaucuauugaaagucagcccucgacacaagg
guuuguc

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<<.<<<........<..<<<.<<.<......<<<<<<<<.>>>>>>>>..
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.>>>>>>.>..................>>>.>>>>>...>>>>...>>>>
>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<<
...<<<<........>>>>.....>>>...<<....>>...<<<<<<<..
....>>>>>>>..<<<<<..<<<...<..........[...>...>>>..
.>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>
>>>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<<....<<<<
<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>
>....>>>>>>>>>...<<.......>>......>>>>>>......>.>>
..<<<<<<....<.<<<....>>>.><<.<<<<<<<........<<<.<<
<<<<<<<...<<<....<<<..<.<<<<..<<<<<.<.....>.>>>>>>
>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.........>>>
>>>>>.>..>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>
>>....<<<......>>>...<<<<<<<...<<<(((.......<<<<<.
....<<..........<<<.<<<<<<<<<<.......<<<<<.<<<...<
<.........>>...>>>.........<<......>>...>>>>>...>>
>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>>>>>>
<<<<<<.<............]..........<.....>............
.......>.>>>>>>....>>>>>>...<<<<<<<<.<<......<<<<.
<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><<.....
<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<<<<
<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<....>
>>..........<<.<<<<<<<<<...>>>>>>>>>>>......>>....
>>>..<<<<<........>>>>>))<<<<....<<<<<..<<<<<<<<..
..>>>>>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<
.<<<<<<<<<<..{{{..>>>>>>....<<<<<.<<<<.<<<<.....<<
<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<.......>>
>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>>..>.......
...>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<...
..>>>>..>>>....<<<<.....<<<<<<<.<<.........<.....<
<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<.>>>>>..>>>>
>>.>>............<<<<<<<<<..<<<.........>>>..<<<<<
<<....<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<
....<<<....<<<<<....>>>>.>...>>>.>>>>..>>>>><<<<<<
.......>>>>>>........<...........<<<<<.......>>>>>
.....>.....>>....>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>
....>>....<<<<<........>>>>>....[[[[[..{{{.{{.....
.[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<<<<..>>>>>>>>>
...<<<<<.....<<<<..<<.....<<...>>....>>...........
...<<<<<<<<...>.>>>>>>>..>>>>..>>>>>....>>>>>>>>>.
.>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<.
..<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>....
>>>>>>>...<<<..<<<<.......>>>>..>>>.<<<....>>>.>>)
)).......((((((..(((..>>>>>>.)))))))))..........]]
]]..}}]]]].......<<.<.<.<<<<<<...<<.......>>...>>>
>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......>>
>>>...>.>.<<<.........>>>.....>>>>>..>...>>>.>>...
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..<<<..<.<<<<<.................>>>>>.><<<<....<<<<
....<<.<<<<<<<}}}.>>>>>..>>.>>...>>>>...>>>><<<<<.
..<<<<<...........>>>>>...>>>>>.>>>...>.>>>>>>....
.<<<<<<<.<<..<<<..<................<.<<<<....>>>>.
>..................<<<..<<<<.......<.<<<<<<<......
>>>>>>>.>.....>>>>..>>>..........>...>>>...>>>>>>>
>><<<<<.<.............>.....<.<<<<<<<.<<.....<<<<.
...<<<<<......>>>>>...>>>>....>>....>>>>.>>>.>...>
>>>>...

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6om0 Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): T2 N3 T4 K5 G6 K7 R8 R9 R12 Y13 F15 S16 F19 H22 G23 K35 K43 G46 T47 Q49 K50 H54 Y57 H58 G59 K60 T61 T68 Q69 H70 N77 K78 V80 K81 L85 K87 R88 R92 K100 S101 S104 F105 R108 V109 K116 Q127 L128 K129 R130 P132 F140 R142
• Binding residue (residue number reindexed from 1): T1 N2 T3 K4 G5 K6 R7 R8 R11 Y12 F14 S15 F18 H21 G22 K34 K42 G45 T46 Q48 K49 H53 Y56 H57 G58 K59 T60 T67 Q68 H69 N76 K77 V79 K80 L84 K86 R87 R91 K99 S100 S103 F104 R107 V108 K115 Q126 L127 K128 R129 P131 F139 R141

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:6om0, PDBe:6om0, PDBj:6om0
• PDBsum: 6om0
• PubMed: 31160784
• UniProt: P46778|RL21_HUMAN Large ribosomal subunit protein eL21 (Gene Name=RPL21)