Structure of PDB 6d9j Chain o Binding Site BS01

Receptor Information
>6d9j Chain o (length=104) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQ
TKPIFRKKAKTTKKIVLRLECVEPNCRSKRMLAIKRCKHFELGGDKKRKG
QVIQ
Ligand information
>6d9j Chain 5 (length=3594) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
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
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PDB6d9j Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES.
Resolution3.2 Å
Binding residue
(original residue number in PDB)
V2 N3 R8 R9 F11 K13 H18 Y26 K28 D31 S32 Y34 G37 R39 R40 R43 K44 G47 Y48 G49 G50 Q51 T52 P54 I55 F56 A60 K61 K80 M82 R87 K89 K97 K98
Binding residue
(residue number reindexed from 1)
V1 N2 R7 R8 F10 K12 H17 Y25 K27 D30 S31 Y33 G36 R38 R39 R42 K43 G46 Y47 G48 G49 Q50 T51 P53 I54 F55 A59 K60 K79 M81 R86 K88 K96 K97
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6d9j, PDBe:6d9j, PDBj:6d9j
PDBsum6d9j
PubMed29856316
UniProtG1T040|RL36A_RABIT Large ribosomal subunit protein eL42 (Gene Name=RPL36A)

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