Structure of PDB 6om0 Chain I Binding Site BS02

Receptor Information

>6om0 Chain I (length=234) Species: 9606 (Homo sapiens)

NPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPP
AINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDV
PTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMG
VPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYND
RYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELA

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

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

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): K34 R35 K37 N38 F39 I41 G42 Q43 I45 Q46 P47 K48 R49 L51 R53 F54 K56 P58 R59 Y60 R73 L74 K110 R113 G139 V140 N141 T142 T145 D162 P163 L166 K187 A188 R192 R196 K197 C199 T200 P244 K245
• Binding residue (residue number reindexed from 1): K6 R7 K9 N10 F11 I13 G14 Q15 I17 Q18 P19 K20 R21 L23 R25 F26 K28 P30 R31 Y32 R45 L46 K82 R85 G111 V112 N113 T114 T117 D134 P135 L138 K159 A160 R164 R168 K169 C171 T172 P216 K217

Gene Ontology

Biological Process

• GO:0042254 ribosome biogenesis

Cellular Component

• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6om0, PDBe:6om0, PDBj:6om0
• PDBsum: 6om0
• PubMed: 31160784
• UniProt: P62424|RL7A_HUMAN Large ribosomal subunit protein eL8 (Gene Name=RPL7A)