Structure of PDB 6om7 Chain T Binding Site BS02

Receptor Information

>6om7 Chain T (length=175) Species: 9606 (Homo sapiens)

MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQ
LKKMKKSSGEIVYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDL
TTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQFHDSKI
KFPLPHRVLRRQHKPRFTTKRPNTF

Ligand information

>6om7 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

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6om7 Structural basis for selective stalling of human ribosome nascent chain complexes by a drug-like molecule.
• Resolution: 3.7 Å
• Binding residue (original residue number in PDB): K2 S4 G5 R8 V67 F68 K70 P72 R74 S86 R87 S88 H91 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 S135 R139 F145 H146 D147 S148 H156 L159 R160 Q162 H163 R166 T168 T169 K170 R171 P172 N173 T174 F175
• Binding residue (residue number reindexed from 1): K2 S4 G5 R8 V67 F68 K70 P72 R74 S86 R87 S88 H91 M93 Y94 R95 R98 R111 G114 A115 R116 H117 R118 R120 S135 R139 F145 H146 D147 S148 H156 L159 R160 Q162 H163 R166 T168 T169 K170 R171 P172 N173 T174 F175

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: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:6om7, PDBe:6om7, PDBj:6om7
• PDBsum: 6om7
• PubMed: 31160784
• UniProt: Q02543|RL18A_HUMAN Large ribosomal subunit protein eL20 (Gene Name=RPL18A)