Structure of PDB 6zvk Chain A2 Binding Site BS01

Receptor Information
>6zvk Chain A2 (length=122) Species: 9986 (Oryctolagus cuniculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVR
KSIARVLTVINQTQKENLRKFYKGKKYKPLDLRPKKTRAMRRRLNKHEES
LKTKKQQRKERLYPLRKYAVKA
Ligand information
>6zvk Chain e2 (length=3920) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgccccccguggggucggcgggggaccguccccc
gaccggcgaccggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggg
gggccccgcgggaccgaaaccccccccgaguguuacagcccccccggcag
cagcacucgccgaaucccggggccgagggagcgagacccgucgccgcgcu
cuccccccucccggcgcccacccggggcgcgccggcgucuccucgugggg
gggccgggccaccccucccacggcgcgaccgcucucccaccccucgucgg
ggggcggggcggacuguccccagugcgccccgggcgggucgcgccgucgg
gcccgggggagguucucucggggccacgcgcgcgucccccgaagaggggg
acggcggagcgagcgcacggggucggcggcgacgucggcuacccacccga
cccgucuugaaacacggaccaaggagucuaacacgugcgcgagucggggg
cucgcacgaaagccgccguggcgcaaugaaggugaaggccggcgcgcucg
ccggccgaggugggaucccgaggccucuccaguccgccgagggcgcacca
ccggcccgucucgcccgccgcgccggggagguggagcacgagcgcacgug
uuaggacccgaaagauggugaacuaugccugggcagggcgaagccagagg
aaacucugguggagguccguagcgguccugacgugcaaaucggucguccg
accuggguauaggggcgaaagacuaaucgaaccaucuaguagcugguucc
cuccgaaguuucccucaggauagcuggcgcucucgcagacccgacgcacc
cccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuuggggc
cgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggc
ucgcuggcgugagccgggcguggaauggagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
gcaggacgguggccauggaagucggaauccgcuaaggaguguguaacaac
ucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgg
gcccauacccggccgucgccggcagucgagaguggacgggagcggcgggg
gcggcgcgcgcgcgcgcccgcccccggagccccgcggacgcuacgccgcg
acgaguaggagggccgcugcggugagccuugaagccuagggcgcgggccc
ggguggagccgccgcaggugcagaucuuggugguaguagcaaauauucaa
acgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcagu
ugaacaugggucagucgguccugagagaugggcgagcgccguuccgaagg
gacgggcgauggccuccguugcccucggccgaucgaaagggagucggguu
cagauccccgaauccggaguggcggagaugggcgccgcgaggcguccagu
gcgguaacgcgaccgaucccggagaagccggcgggagccccggggagagu
ucucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgag
agaggggcccgugccuuggaaagcgucgcgguuccggcggcguccgguga
gcucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgcc
gggccguacccauauccgcagcaggucuccaaggugaacagccucuggca
uguuggaacaauguagguaagggaagucggcaagccggauccguaacuuc
gggauaaggauuggcucuaagggcugggucggucgucggccggcgccuag
cagccgacuuagaacuggugcggaccaggggaauccgacuguuuaauuaa
aacaaagcaucgcgaaggcccgcggcggguguugacgcgaugugauuucu
gcccagugcucugaaugucaaagugaagaaauucaaugaagcgcggguaa
acggcgggaguaacuaugacucucuuaagguagccaaaugccucgucauc
uaauuagugacgcgcaugaauggaugaacgagauucccacugucccuacc
uacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucagcg
gggaaagaagacccuguugagcuugacucuagucuggcacggugaagaga
caugagagguguagaauaagugggaggcccccggcgcccccccggugucc
ccgcgaggggcccggggcgggguccgccggcccugcgggccgccggugaa
auaccacuacucugaucguuuuuucacugacccggugaggcgggggggcg
agccccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccgg
ccgggcgcgacccgcuccggggacagugccagguggggaguuugacuggg
gcgguacaccugucaaacgguaacgcagguguccuaaggcgagcucaggg
aggacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuug
auuuucaguacgaauacagaccgugaaagcggggccucacgauccuucug
accuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaa
cuggcuuguggcggccaagcguucauagcgacgucgcuuuuugauccuuc
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccuguccccgccggcgccgcg
cgccgggaccgggguccggugcggagugcccuucguccugggaaacgggg
cgcggccggagaggcggccgcccccucgcccgucacgcaccggccguucg
uggggaaccuggcgcuaaaccauucguagacgaccugcuucugggucggg
guuucguacguagcagagcagcucccucgcugcgaucuauugaaagucag
cccucgacacaaggguuugu
.........................<<<<<<<....<......>.....>
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[....<<<...<<<<<<<<<<<...>>>>>>>.>>>>...
..>>>....<<<<<<<<<....<<<<<<<<.<.<....<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>>.>>>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<..
....<<<<<<<<.<<<.....<<<<<<<<<<<...<<<.....<<<<.<<
....<<<<.<<<..<<<<<<<<<<..>>>>..>>>>>>>>>>>>>>>.>>
>>.......>>>.>>>>>>>>>>>......>>>.>>>.>>>>>..<<<<<
<<..<<<<<<<<<<.<<<....<.....<<<<.<<<<......<<<<<<<
.<....<..>...........>>..>>>>>>.......>>>>.>>>>...
.......>.>>>...>>>>>>>>>>....................<<<<.
..<<<<<<<..<<<<<....<<<.>>>..>>>>>.<<......>>.>>>>
>>>.....<<.<<<<.<<<<<<<<<<<<<<<<<.......<<<<.....>
>>>.<<<<<<<.<<<<....>>>>.>>>>>>>>>>.>>>>>>>>>>>.>>
>...>.>>>...........>.>.........<<<<<<<<.....>>>>>
>>>.........>>>>.......>>.>>>>>....>>>...>>>>>>>>.
.<<<<........>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<
<<........>>>>.....>>>...<<....>>...<<<<<<<......>
>>>>>>..<<<<<...<<<..<<<...(((..[..>>>..>>>....>>>
>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>
>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<<<<.
...>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>>...
.>>>>>>>>>...<<.......>>......>>>>>>...>..>.>>..<<
<<<<....<.<<<....>>>.><<<<<<<<<<..................
.........<<.<<<<<<<<<...<<<....<<<..<.<<<..<....<.
........>...>.>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<
<<........>>>>>>>>>...>>.>>>>>>>>>.>>>..<<<<.<<<<<
.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((
.......<<<<<.....<<..........<<<.<<<<<<<<<<.......
<<....<<....<<.........>>....>>.......<.<<......>>
.>....>>...>>>>>>>>>>>>>..........))).>>...>>>>>..
>>>...>>>>>>><<<<<<.<<<............].)))..........
............................................>>>>>>
>>>....>>>>>>.<<<<<<<<<<.<<......<<<<.<<<<....>>>>
>>>>...>>>>>>>>>>.>>.....>>>>>><<<....<<.....<<<<<
<.......>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<.....
>>.>>>>>>....((<<<<<<...<<....<<<....>>>..........
<<.<<<<<<<<<...>>>>>>>>>>>......>>....>>>..<<<<<..
......>>>>>))<<<<....<<<<...<<<<<<<<....>>>>>>>>..
<<<....>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<.
.{{{..>>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>...
..>>>>>>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>...
>>>>>>>>>>>>.........>>>>>>>..>..........>..>>>.>>
>>.>>>..>>.....<<......>>>>>>>.<<<<.....>>>>..>>>.
...<<<<.....<<<<<<<.<<.........<.....<<<<<....<<..
>>.....>>>>><<.<<<<<<<<<<<..<<<<<<<.>>>>>>>.......
>>>>>..>>>>>>.>>............<<<<<<<<<..<<<........
.>>>..<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..
<<<..<<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..
>>>>><<<<<<.......>>>>>>........<...........<<<<<.
......>>>>>.....>.....>>....>>.>>>>>>>..>..>>.>>>>
>>>..>>>>>>...>>>....<<<<<........>>>>>....[[[[[..
{{{.{{......[[[[.{{[[[[..<<<<<.<<<<<<<<<.<<<<<<.<<
<...............................<<<<.<<<<<<<<.<<<<
<.....>>>>>>>>>>>..>>...>>>>......................
.................>>>.>>>>>>...<<<<<.....<<<<..<<.<
<<<<<<..>>>>>>>>>..............<<<<<<<<<<<.....>>>
>>>>>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<<...
..>>>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<
<<<.......>>>>>>.....<<.[.(((>>....>>>>>>>...<<<..
<<<<.......>>>>..>>>.<<<....>>>.>>)))]......((((((
..(((..>>>>>>.)))))))))..........]]]]..}}]]]].....
..<<.<.<.<<<<<<...<<.......>>...>>>>>>...>>.>.>...
....<<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<..
.......>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>
.>>>>....}}..}}}.]]]]].....<<<<<<....<<<..<.<<<<<.
................>>>>>.><<<<....<<<<....<<.<<<<<<.}
}}..>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<........
...>>>>>...>>>>>.>>>.....>>>>>>.....<<<<<<<.....<<
<.....<<.........<<<<<..<.<<....<<<<<.<<<<<..>>>.>
>...>>>>>..>>>.>>>>>........>>....<<..<<<<....<<<<
.<<<<<<<......>>>>>>>>>>>...>>>>..>>..............
..>>>....>>>>>>><<<<<.<.............>....<<.<<<<<<
<.<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>....
>>>>.>>>.>>..>>>>>..
Receptor-Ligand Complex Structure
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PDB6zvk The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism.
Resolution3.49 Å
Binding residue
(original residue number in PDB)
R70 K74 Y78 K79 K87 R94 K97 K106 R109 K110 R112
Binding residue
(residue number reindexed from 1)
R69 K73 Y77 K78 K86 R93 K96 K105 R108 K109 R111
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003729 mRNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006412 translation
Cellular Component
GO:0005737 cytoplasm
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:6zvk, PDBe:6zvk, PDBj:6zvk
PDBsum6zvk
PubMed33296660
UniProtG1SIT5|RL35_RABIT Large ribosomal subunit protein uL29 (Gene Name=RPL35)

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