Structure of PDB 6d9j Chain e Binding Site BS01

Receptor Information

>6d9j Chain e (length=128) Species: 9986 (Oryctolagus cuniculus)

AALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKG
QILMPNIGYGSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAH
NVSSKNRKAIVERAAQLAIRVTNPNARL

Ligand information

>6d9j Chain 5 (length=3594)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccgccccggcagcagcagcucgccgaaucccggggccgagggagcgaga
cccgugcgccgcgcucuccccccucgggggggccgggccaccccucccac
ggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgcc
gucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggc
gaugucggcuacccacccgacccgucuugaaacacggaccaaggagucua
acacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggu
gaaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgc
cgagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagc
acgagcgcacguguuaggacccgaaagauggugaacuaugccugggcagg
gcgaagccagaggaaacucugguggagguccguagcgguccugacgugcg
aaucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucu
aguagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgc
aguuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgauc
ucaaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugu
ggagccgggcguggaaugcgagugccuagugggccacuuuugguaagcag
aacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccg
acgcucaucagaccccagaaaagguguugguugauauagacagcaggaug
guggccauggaagucggaauccgcuaaggaguguguaacaacucaccugc
cgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauac
ccggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgc
uacgccgcgacgaguaggagggccgcugcggugagccuugaagccuaggg
cgcgggcccggguggagccgccgcaggugcagaucuuggugguaguagca
aauauucaaacgagaacuuugaaggccgaaguggagaaggguuccaugug
aacagcaguugaacaugggucagucgguccugagagaugggcgagcgccg
uuccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggg
agucggguucagauccccgaauccggaguggcggagaugggcgccgcgag
gcguccagugcgguaacgcgaccgaucccggagaagccggcgggagcccc
ggggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguu
cgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggc
guccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaa
ucucgcgccgggccguacccauauccgcagcaggucuccaaggugaacag
ccucuggcauguuggaacaauguagguaagggaagucggcaagccggauc
cguaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaa
cuggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcg
aaggcccgcggcggguguugacgcgaugugauuucugcccagugcucuga
augucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaac
uaugacucucuuaagguagccaaaugccucgucaucuaauuagugacgcg
caugaauggaugaacgagauucccacugucccuaccuacuauccagcgaa
accacagccaagggaacgggcuuggcggaaucagcggggaaagaagaccc
uguugagcuugacucuagucuggcacggugaagagacaugagagguguag
aauaagugggaggcccgggccgccggugaauaccacuacucugaucguuu
uuucacugacccggugaggcgggggggcgagccgggcucucgcuucuggc
gccaagcgcccggccggccgggcgcgacccgcuccggggacagugccagg
uggggaguuugacuggggcgguacaccugucaaacgguaacgcagguguc
cuaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaa
aagcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggg
gccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaa
aguuaccacagggauaacuggcuuguggcggccaagcguucauagcgacg
ucgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaa
uucaccaagcguuggauuguucacccacuaauagggaacgugagcugggu
uuagaccgucgugagacagguuaguuuuacccuacugaugauguguuguu
gccaugguaauccugcucaguacgagaggaaccgcagguucagacauuug
guguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauag
cgccggagccucgguuggccucggauagccggucccccgccgggguccgg
ugcggagagcccuucgucccgggaaacggggcggccggaaagggggccgc
ccucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacc
auucguagacgaccugcuucugggucgggguuucguacguagcagagcag
cugcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6d9j Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): L7 V8 K9 K14 K15 R16 K18 K19 F20 R22 Q24 D26 Y28 V29 K30 N34 R36 K37 G40 D42 N43 R44 R47 K50 P56 N57 I58 G59 Y60 G61 S62 K67 H68 M69 P71 E98 H101 N102 S104 K106 N107 N124 A127 R128
• Binding residue (residue number reindexed from 1): L6 V7 K8 K13 K14 R15 K17 K18 F19 R21 Q23 D25 Y27 V28 K29 N33 R35 K36 G39 D41 N42 R43 R46 K49 P55 N56 I57 G58 Y59 G60 S61 K66 H67 M68 P70 E97 H100 N101 S103 K105 N106 N123 A126 R127

Gene Ontology

Molecular Function

• 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:6d9j, PDBe:6d9j, PDBj:6d9j
• PDBsum: 6d9j
• PubMed: 29856316
• UniProt: G1TUN8|RL32_RABIT Large ribosomal subunit protein eL32 (Gene Name=RPL32)