Structure of PDB 6ip5 Chain 2D Binding Site BS01

Receptor Information

>6ip5 Chain 2D (length=213) Species: 9606 (Homo sapiens)

GRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLGGH
MVSDEYEQLSSEALEAARICANKYMVKSCGRDGFHMRVRLHPFHVIRINK
MLSCAGADRLQTGMRGAFGKPQGTVARVHIGQVIMSIRTKLQNEEHVIEA
LRRAKFKFPGRQKIHISKKWGFTKFNADEFEDMVAKKCLIPDGCGVKYVP
SHGPLDKWRVLHS

Ligand information

>6ip5 Chain 1A (length=3717)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuu
ggggccgaaacgaucucaaccuauucucaaacuuuaaauggguaagaagc
ccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggcc
acuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguua
aggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugau
auagacagcaggacgguggccauggaagucggaauccgcuaaggagugug
uaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugga
gcgucgggcccauacccggccgucgccggcagucgagaguggacgggagc
ggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccgc
ugcggugagccuugaagccuagggcgcgggcccggguggagccgccgcag
gugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaaggc
cgaaguggagaaggguuccaugugaacagcaguugaacaugggucagucg
guccugagagaugggcgagcgccguuccgaagggacgggcgauggccucc
guugcccucggccgaucgaaagggagucggguucagauccccgaauccgg
aguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccgau
cccggagaagccggcgggagccccggggagaguucucuuuucuuugugaa
gggcagggcgcccuggaauggguucgccccgagagaggggcccgugccuu
ggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuug
aaaauccgggggagaggguguaaaucucgcgccgggccguacccauaucc
gcagcaggucuccaaggugaacagccucuggcauguuggaacaauguagg
uaagggaagucggcaagccggauccguaacuucgggauaaggauuggcuc
uaagggcugggucggucgucggccggcgccuagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggaguaacuau
gacucucuuaagguagccaaaugccucgucaucuaauuagugacgcgcau
gaauggaugaacgagauucccacugucccuaccuacuauccagcgaaacc
acagccaagggaacgggcuuggcggaaucagcggggaaagaagacccugu
ugagcuugacucuagucuggcacggugaagagacaugagagguguagaau
aagugggaggcccgggccgccggugaaauaccacuacucugaucguuuuu
ucacugacccggugaggcgggggggcgagccccgaggggcucucgcuucu
ggcgccaagcgcccggccgcgcgccggccgggcgcgacccgcuccgggga
cagugccagguggggaguuugacuggggcgguacaccugucaaacgguaa
cgcagguguccuaaggcgagcucagggaggacagaaaccucccguggagc
agaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccg
ugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcaggag
gugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguu
cauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauug
ugaagcagaauucaccaagcguuggauuguucacccacuaauagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugaug
auguguuguugccaugguaauccugcucaguacgagaggaaccgcagguu
cagacauuugguguaugugcuuggcugaggagccaauggggcgaagcuac
caucugugggauuaugacugaacgccucuaagucagaaucccgcccaggc
ggaacgauacggcagcgccgcggagccucgguuggccucggauagccggu
cccccgcgggguccggugcggagugcccuucguccugggaaacggggcgc
ggccggagaggcggccgcccccucgcccgucacgcaccgcacguucgugg
ggaaccuggcgcuaaaccauucguagacgaccugcuucugggucgggguu
ucguacguagcagagcagcucccucgcugcgaucuauugaaagucagccc
ucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ip5 HCV IRES Captures an Actively Translating 80S Ribosome.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): R3 R4 P5 A6 R7 C8 N14 K15 F22 D35 E63 K74 R90 F94 R98 I99 C105 G114 M115 R116 A118 Q133 R154 F157 K158 P160 K175 G194 K198
• Binding residue (residue number reindexed from 1): R2 R3 P4 A5 R6 C7 N13 K14 F21 D34 E62 K73 R89 F93 R97 I98 C104 G113 M114 R115 A117 Q132 R153 F156 K157 P159 K174 G193 K197

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0006412 translation
• GO:0007141 male meiosis I
• GO:0007283 spermatogenesis
• GO:0030154 cell differentiation
• GO:0051321 meiotic cell cycle

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6ip5, PDBe:6ip5, PDBj:6ip5
• PDBsum: 6ip5
• PubMed: 31080011
• UniProt: Q96L21|RL10L_HUMAN Ribosomal protein uL16-like (Gene Name=RPL10L)