Structure of PDB 7nwi Chain L Binding Site BS01

Receptor Information

>7nwi Chain L (length=210) Species: 9986 (Oryctolagus cuniculus)

APSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPA
SGPLRPIVRCPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPR
RRNKSTESLQANVQRLKEYRSKLVLFPRKPSAPKKGDSSAEELKLATQLT
GPVMPIRNVFKKEKARVITEEEKNFKAFASLRMARANARLFGIRAKRAKE
AAEQDVEKKK

Ligand information

>7nwi Chain 5 (length=3662)

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
ccuguugagcuugacucuagucuggcacggugaagagacauguuuuuuca
cugacccggugaggcgggggggcgagccccgaggggcucucgcuucuggc
gccaagcgcccggccgcgcgccggccgggcgcgacccgcuccggggacag
ugccagguggggaguuugacuggggcgguacaccugucaaacgguaacgc
agguguccuaaggcgagcucagggaggacagaaaccucccguggagcaga
agggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccguga
aagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucau
agcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauuguga
agcagaauucaccaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaug
uguuguugccaugguaauccugcucaguacgagaggaaccgcagguucag
acauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccau
cugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgga
acgauacggcagcgccgcggagccucgguuggccucggauagccgguccc
ccgcgggguccggugcggagugcccuucguccugggaaacggggcgcggc
cggagaggcggccgcccccucgcccgucacgcacgccguucguggggaac
cuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgua
cguagcagagcagcucccucgcugcgaucuauugaaagucagcccucgac
acaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7nwi Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA.
• Resolution: 3.13 Å
• Binding residue (original residue number in PDB): R5 M8 H13 F14 H15 K16 Q28 R31 R35 R36 R39 R42 R44 R56 V59 R60 P62 R65 Y66 H67 R71 R74 L78 K88 R92 P100 R101 R102 R103 K105 S106 R129 V160 K163 K165 F179 R183 M184 R186 N188 R198
• Binding residue (residue number reindexed from 1): R4 M7 H12 F13 H14 K15 Q27 R30 R34 R35 R38 R41 R43 R55 V58 R59 P61 R64 Y65 H66 R70 R73 L77 K87 R91 P99 R100 R101 R102 K104 S105 R128 V159 K162 K164 F178 R182 M183 R185 N187 R197

Gene Ontology

Molecular Function

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

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:7nwi, PDBe:7nwi, PDBj:7nwi
• PDBsum: 7nwi
• PubMed: 34157102
• UniProt: G1TKB3|RL13_RABIT Large ribosomal subunit protein eL13 (Gene Name=RPL13)