Structure of PDB 6ip8 Chain 2x Binding Site BS01

Receptor Information
>6ip8 Chain 2x (length=146) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYK
LLEPVLLLGKERFAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYV
DEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARARYQKSYR
Ligand information
>6ip8 Chain 2m (length=1742) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgcuccucucccacuuggauaa
cugugguaauucuagagcuaauacaugccgacgggcgcugacccccuucg
cgggggggaugcgugcauuuaucaguggugacucuagauaaccucgggcc
gaucgcacgccccccguggcggcgacgacccauucgaacgucugcccuau
caacuuucgaugguagucgccgugccuaccauggugaccacgggugacgg
ggaaucaggguucgauuccggagagggagccugagaaacggcuaccacau
ccaaggaaggcagcaggcgcgcaaauuacccacucccgacccggggaggu
agugacgaaaaauaacaauacaggacucuuucgaggcccuguaauuggaa
ugaguccacuuuaaauccuuccgcgaggauccauuggagggcaagucugg
ugccagcagccgcgguaauuccagcuccaauagcguauauuaaaguugcu
gcaguuaaaaagcucguaguuggaucuugggagcgggcguccccgccgcc
ucucggccggggcccgaagcauuuacuuugaaaaaauuagaguguucaaa
gcaggcccgagccgccuggauaccgcagcuaggaauaauggaauaggacc
gcgguucuauuuuguugguuuucggaacugaggccaugauuaagagggac
ggccgggggcauucguauugcgccgcuagaggugaaauucuuggaccggc
gcaagacggaccagagcgaaagcauuugccaagaauguuuucauuaauca
agaacgaaagucggagguucgaagacgaucagauaccgucguaguuccga
ccauaaacgaugccgacuggcgaugcggcggcguuauucccaugacccgc
cgggcagcuuccgggaaaccaaagucuuuggguuccggggggaguauggu
ugcaaagcugaaacuuaaaggaauugacggaagggcaccaccaggagugg
agccugcggcuuaauuugacucaacacgggaaaccucacccggcccggac
acggacaggauugacagauugauagcucuuucucgauuccguggguggug
gugcauggccguucuuaguugguggagcgauuugucugguuaauuccgau
aacgaacgagacucuggcaugcuaacuaguuacgcgacccccgagcgguc
ggcgucccccaacuucuuagagggacaaguggcguucagccacccgagau
ugagcaauaacaggucugugaugcccuuagauguccggggcugcacgcgc
gcuacacugacuggcucagcgugugccuacccuacgccggcaggcgcggg
uaacccguugaaccccauucgugauggggaucggggauugcaauuauucc
ccaugaacgaggaauucccaguaagugcgggucauaagcuugcguugauu
aagucccugcccuuuguacacaccgcccgucgcuacuaccgauuggaugg
uuuagugaggcccucggaucggccccgccggggucggcccacggcccugg
cggagcgcugagaagacggucgaacuugacuaucuagaggaaguaaaagu
cguaacaagguuuccguaggugaaccugcggaaggaucauua
...<<<<....((((.>>>><<<.<<<<<<...<.<<..<......<<<.
<<<..<<....<<....<<..........>>...>>.>>......<<...
.....<<<.<....<<....<<.....................<<.....
<<..<<.....>>..>>......>>.........<<<<...<<<<<....
..>>>>>...>>>>....<<<<<.............>>>>>.........
..<<<<.<<<<......>>>>>>>>.....>>...>>..>.>>>.<<<..
..<<<....<<<<<<<.........>>>>>>>>>>......>>>...<<<
.<<<<....>>>>....>>>.>>.<<.<<<..........>>>.>>.<.<
<....>>.>...>>>>>>.........<<<....<<<.....>>>..>>>
..>...>>.>.....<<...<<<<............>>.>>....>>...
...<<..<...........>..>>.........<<<<<((......<<<<
.....<<..))>>.......>>>>.>>>>>..>>>>>>.>>>........
.<.<((.....<.<<...<<<..<..........................
......................<<<<<<.<.......<<...<.......
>.<<<<.......>>>>...>>......>.>>>..>>>.......<<...
.<.<<<<................>>.>>.>...>>....>.....<<<<<
<..<...<<<<..<<..<<<<<<<<...<<<......>>>......>>>>
>>>.>.>>.......<<....>>...>>>>..>..>>>.>>>...>>>..
.>>.>....<<<<<<....<...<<<<.........>>>>...>.>>>>>
>..........<<<.<<.<<<..<.<<<<<<.<<<........>>>>>>>
>>.>..>>>...<<..))>>...>>.....>>>.>.>.<<<......<<<
<....>>>>....>>>..))))..<<<<<.<<<<<<<..<<..<<<<<..
<<<.<<<<........<<........>>..........<<<<<......<
<<<<........<<..<<........>>..>>......>>>>>...<<.<
<<...<.<<<<<<....<<<.<<<<<....>>>...<<<......>>>..
.>>.>>>....<<<...<...<<<<..<<<...........<........
>..........>>>..>>>>..>.....<<<<<.....>>>>>.......
.>>>....>>>.>>>.....>.>>>>>.......>>>>>......>>>>.
>>>.....<<.<<<................<<<.<<<<....>>>>.>>>
..............>>>.>>......<.....<<<<<..........>>>
>>.....>.....>>>>>.....<<<<<<<<.......>>>>>>>>....
..>>...>>>>>>>>>>.>>.......<<.<..<<<<.<<....<<<<<<
<<.<<<..<<<<.<<...<<<<<.<..<<...................>>
..>...>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>...>.
>>..........<<<<<<<<....>>>>>>>>..........
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6ip8 HCV IRES Captures an Actively Translating 80S Ribosome.
Resolution3.9 Å
Binding residue
(original residue number in PDB)		M1 L7 Q11 F13 R15 K16 K17 T18 V22 H24 K26 K33 R37 I42 R45 R69 R71 G74 G75 G76 H77 V78 A79 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 A139 R140 Y141 Q142 K143 S144 R146
Binding residue
(residue number reindexed from 1)		M1 L7 Q11 F13 R15 K16 K17 T18 V22 H24 K26 K33 R37 I42 R45 R69 R71 G74 G75 G76 H77 V78 A79 R125 R126 C127 E128 S129 K130 K131 F132 G136 A137 R138 A139 R140 Y141 Q142 K143 S144 R146
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
Biological Process
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0002181 cytoplasmic translation
GO:0006364 rRNA processing
GO:0006412 translation
GO:0042274 ribosomal small subunit biogenesis
GO:1990830 cellular response to leukemia inhibitory factor
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0005925 focal adhesion
GO:0015935 small ribosomal subunit
GO:0016020 membrane
GO:0022626 cytosolic ribosome
GO:0022627 cytosolic small ribosomal subunit
GO:0032040 small-subunit processome
GO:0045202 synapse
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6ip8, PDBe:6ip8, PDBj:6ip8
PDBsum6ip8
PubMed31080011
UniProtP62249|RS16_HUMAN Small ribosomal subunit protein uS9 (Gene Name=RPS16)

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