Structure of PDB 6om7 Chain H Binding Site BS02

Receptor Information

>6om7 Chain H (length=225) Species: 9606 (Homo sapiens)

NFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHKEYRQMYRTEIRMAR
MARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFV
KLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNA
LIARSLGKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKK
TTHFVEGGDAGNREDQINRLIRRMN

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

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

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): N24 F25 K31 R32 L33 K35 Q39 R43 R47 K48 Y51 E52 H58 Y61 R62 Q63 Y65 R66 R70 R73 M74 R76 K77 R96 G97 I98 N99 P103 K107 L111 R113 I117 A128 N131 M132 N146 L147 K148 N151 K156 R157 K165 R166 Y182 E188 K202 N206 K212 L213 S214 S215 P216 R217 G219 M220 K222 K223 R242 R245
• Binding residue (residue number reindexed from 1): N1 F2 K8 R9 L10 K12 Q16 R20 R24 K25 Y28 E29 H35 Y38 R39 Q40 Y42 R43 R47 R50 M51 R53 K54 R73 G74 I75 N76 P80 K84 L88 R90 I94 A105 N108 M109 N123 L124 K125 N128 K133 R134 K142 R143 Y159 E165 K179 N183 K189 L190 S191 S192 P193 R194 G196 M197 K199 K200 R219 R222

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0042802 identical protein binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• 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: P18124|RL7_HUMAN Large ribosomal subunit protein uL30 (Gene Name=RPL7)