Structure of PDB 6d9j Chain G Binding Site BS01

Receptor Information
>6d9j Chain G (length=233) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKV
PPAINQFTQVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAKRP
PVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCI
LKGKARLCRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTNYNDRYDEI
RRHWGGNVLGPKSVARIAKLEKAKAKELATKLG
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
.........................<<<<<<.....<......>......
>>>>>.>.........<<....>>...<<<<<.....<<.....>>....
>>>>>...[[[....<<<...<<.<<<<<<<.....>>>>>>..>>>...
..>>>....<<<<<<<<<....<<<<<<<<..<<<<<<<.....<<<<..
....>>>>.....((......<<<.....))>>>.....>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...(((((..<<<<<<)))))..]]]........................
..........<<....>>...............<<<<....>>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<.
<<<<<<<<<......>>>>>>>>>>>>>>>>>>>>>>>>>...>>>..>>
>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<.<<
<<...<<..<<<.<...<<<......<<<<<<<<.>>>>>>>>.......
>>>..>..>>>.........>>>>>>...>>>>>>>>>>...........
..............<...<<<<<<..>>>>>>....<<<...<<.<<<<<
<<<<<<<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>.>>>>>>>>>
>>.>>>...>>.>>.>................>........>>>.>>>>>
....>>>>...>>>>>>>>..<<<<........>>>><<<<<<...<<<<
<<<<<<<<<<..<<<...<<<<.....>>>>.....>>>...<<....>>
...<<<<<<.....>>>>>>..<<<<<...<<<..<<<....[[.[..>>
>..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>
....>>>>>>>>>>>>>>.<<.<...<<<<<<.....<<<<<<<<<..<<
<....<<<<<<<....>>>>>>>.....>>>...<<<<.<<.<<......
..>>>>>>>>....>>>>>>>>>...<<.......>>......>>>>>>.
.....>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<...<<
<.<<<<<<<<<...<<<....<<<....<<<..<<<<.<.........>.
>>>>>>>....>>>..>>.>...>>>>>>>...<<<<<<<<<.<......
>>>>>>>>>>....>>>>>>>>>>>>.>>>..<<<<.<<<<<.....>>>
>>.>>>>....<<<......>>>...<<<<<<<...<<<(((.......<
<<<<.....<<..........<<<.<<<<<<<<<<.......<<<<<.<<
....<<.........>>....>>.........<<......>>...>>>>>
...>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>
>>>>><<<<<<.<<<.....................].]]..........
...>>>>>>>>>....>>>>>>...<<<<<<<<.<<......<<<<.<<<
......>>>>>>>...>>>>>>>>>>........>>>>>><<.....<<.
....<<<<<<.......>>>>>>.<<<.....<<<<..<<...<<<<<<.
..<<.....>>.>>>>>>....((<<<<<<...<<..<.<<<....>>>>
.........<<.<<<<<..<.....>..>>>>>>>......>>....>>.
..<<<<<........>>>>>))<<<<....<<<<<...<<<<<<<....>
>>>>>>...<<<....>>>......<<<<<<<...<<<<<<<<<<<<<<<
<<<<<<<<.......>>>>>>.....<<<<.<<<<.<<<<.....<<...
....>>.....>>>>>>>>..>>>>......<<<<<<<.......>>>>>
>>>>>>.>.>>>>>>>>>>>>.........>>>>>>>.............
>>.>>>.>>>>>>>>..>>.....<<......>>.>>>>.<<<<.....>
>>>..>>>....<<<<.....<<<<<<..<<...............<<<<
<...............>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.
>>............<<<<<<<<<..<<<.........>>>..<<<<<<<.
...<<<<.....>>>>......>>>>>>>...<<..<<<..<<<<<<.<.
.<<<....<<<<<....>>>>.>...>>>>>>>>..>>>>><<<<<....
.....>>>>>........<...........<<<<<.......>>>>>...
..>.....>>....>>.>>>>>>>.....>>..>>>>>>..>>>>>>...
.>>....<<<<<........>>>>>....[[[[[..{{{.{{......[[
[[.{.[[[[..<<<<..<<<<<<<<..<<<<<<<<<<<<.<<<<......
....<<<.<..<<<<..>>>>...........>.>>>.>>>>.>>.>>>>
>>>>>>...<<<<<.....<<<<..<<.<<<<<>.>>>>>>.........
.....<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>.....>>>>>>>
>...>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<
<...<<<<<<<...<<<<<<.......>>>>>>.....<<...(((>>..
..>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>
>))).......((((((..(((..>>>>>>.)))))))))..........
]]]]...}]]]].......<<..<..<<<<<<...<<.......>>...>
>>>>>....>.>.>.........<<<.<<<<<<..<.<.<<<<<......
>>>>>...>.>.<<<.........>>>.....>>>>>..>...>>>....
...<<<<<<<....>>>.>>>>....}}..}}}.]]]]].....<.<<<<
.<..<<<..<.<<<<<.................>>>>>.><<<<....<<
<<.....<.<<<<<<<....>>>>>..>>.>....>>>>...>>>><<<<
....<<<<<...........>>>>>....>>>>.>>>...>.>>>>.>.<
<<<<<...<<<<....<<<........<<<<<..<<<<<.>>>>>.>>>>
>.......>>>...<<<..<<<<....<<.<<<<<<........>>>>>>
..>>...>>>>..>>>..............>>>>....>>>>>>.<<<<<
.<.............>....<<.<<<<<<<.<<.....<<<<....<<<<
<.>>>>>...>>>>....>>....>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)
K87 R88 K90 N91 F92 I94 I98 P100 K101 R102 R106 F107 K109 R112 Y113 R115 K125 R126 L127 K160 Q161 K163 R166 R185 P186 G192 V193 N194 T195 R249 K250 T253 L295 P297 K298 S299 R302
Binding residue
(residue number reindexed from 1)
K8 R9 K11 N12 F13 I15 I19 P21 K22 R23 R27 F28 K30 R33 Y34 R36 K46 R47 L48 K81 Q82 K84 R87 R99 P100 G106 V107 N108 T109 R163 K164 T167 L209 P211 K212 S213 R216
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:6d9j, PDBe:6d9j, PDBj:6d9j
PDBsum6d9j
PubMed29856316
UniProtG1STW0|RL7A_RABIT Large ribosomal subunit protein eL8 (Gene Name=RPL7A)

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