Structure of PDB 6p5i Chain AZ Binding Site BS01

Receptor Information

>6p5i Chain AZ (length=135) Species: 9986 (Oryctolagus cuniculus)

GKFMKPGKVVLVLAGRYSGRKAVIVKNIDDGTSDRPYSHALVAGIDRYPR
KVTAAMGKKKIAKRSKIKSFVKVYNYNHLMPTRYSVDIPLDKTVVNKDVF
RDPALKRKARREAKVKFEERYKTGKNKWFFQKLRF

Ligand information

>6p5i Chain 5 (length=3594)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugccggcggggcgga
ucucccgcucccgucggcgggggaccgccccccggccggcgaccggccgc
cgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacg
gcugggaaggcccggcggggaagguggcccgggggccccggguguuacag
cccacccggcagcagcagcucgccgaaucccggggccgagggagcgagac
cugugucgccgcgcucuccccccugggggggccgggccaccccucccacg
gcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgucccccgcgagcgcacggggucggcggcg
augucggcuacccacccgacccgucuugaaacacggaccaaggagucuaa
cacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaaggug
aaggccggcgccgccggccgaggugggaucccgaggccuuccaguccgcc
gagggcgcaccaccggcccgucucgcccgccgcgccggggagguggagca
cgagcgcacguguuaggacccgaaagauggugaacuaugccugggcaggg
cgaagccagaggaaacucugguggagguccguagcgguccugacgugcga
aucggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucua
guagcugguucccuccaaaguuucccucaggauagcuggcgcucuccgca
guuuuauccgguaaagcgaaugauuagaggucuuggggccgaaacgaucu
caaccuauucucaaacuuuaaauggguaagaagcccggcucgcuggugug
gagccgggcguggaaugcgagugccuagugggccacuuuugguaagcaga
acuggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccga
cgcucaucagaccccagaaaagguguugguugauauagacagcaggaugg
uggccauggaagucggaauccgcuaaggaguguguaacaacucaccugcc
gaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacc
cggccgucgcuggcagucggcagagcgagaaagagaguggcgcggacgcu
acgccgcgacgaguaggagggccgcugcggugagccuugaagccuagggc
gcgggcccggguggagccgccgcaggugcagaucuuggugguaguagcaa
auauucaaacgagaacuuugaaggccgaaguggagaaggguuccauguga
acagcaguugaacaugggucagucgguccugagagaugggcgagcgccgu
uccgaagggacgggcgauggccuccguugcccucagccgaucgaaaggga
gucggguucagauccccgaauccggaguggcggagaugggcgccgcgagg
cguccagugcgguaacgcgaccgaucccggagaagccggcgggagccccg
gggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguuc
gccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggcg
uccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaau
cucgcgccgggccguacccauauccgcagcaggucuccaaggugaacagc
cucuggcauguuggaacaauguagguaagggaagucggcaagccggaucc
guaacuucgggauaaggauuggcucuaagggcuggcagccgacuuagaac
uggugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcga
aggcccgcggcggguguugacgcgaugugauuucugcccagugcucugaa
ugucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacu
augacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgc
augaauggaugaacgagauucccacugucccuaccuacuauccagcgaaa
ccacagccaagggaacgggcuuggcggaaucagcggggaaagaagacccu
guugagcuugacucuagucuggcacggugaagagacaugagagguguaga
auaagugggaggcccgggccgccggugaaauaccacuacucugaucguuu
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: 6p5i The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
• Resolution: 3.1 Å
• Binding residue (original residue number in PDB): G16 R17 R36 Y38 R48 R51 K52 T54 A55 K59 K64 R65 K67 K69 K73 V74 N76 N78 H79 K107 R111 R112 K115 K133 R135 F136
• Binding residue (residue number reindexed from 1): G15 R16 R35 Y37 R47 R50 K51 T53 A54 K58 K63 R64 K66 K68 K72 V73 N75 N77 H78 K106 R110 R111 K114 K132 R134 F135

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006364 rRNA processing
• GO:0006412 translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6p5i, PDBe:6p5i, PDBj:6p5i
• PDBsum: 6p5i
• PubMed: 31609474
• UniProt: G1TXF6|RL27_RABIT Large ribosomal subunit protein eL27 (Gene Name=RPL27)