Structure of PDB 6ip6 Chain 3L Binding Site BS01

Receptor Information
>6ip6 Chain 3L (length=140) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVISLGPQVAEGENVFGVCHIFASFNDTFVHVTDLSGKETICRVTGGMK
VKADRDESSPYAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPG
AQSALRALARSGMKIGRIEDVTPIPSDSTRRKGGRRGRRL
Ligand information
>6ip6 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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PDB6ip6 HCV IRES Captures an Actively Translating 80S Ribosome.
Resolution4.5 Å
Binding residue
(original residue number in PDB)
H32 N38 D39 F41 H43 G49 K50 E51 T52 R55 T57 G59 M60 D65 R66 E68 R98 I135 P136 S137 D138 S139 T140 R141 K143 R146 R147 R149 R150 L151
Binding residue
(residue number reindexed from 1)
H21 N27 D28 F30 H32 G38 K39 E40 T41 R44 T46 G48 M49 D54 R55 E57 R87 I124 P125 S126 D127 S128 T129 R130 K132 R135 R136 R138 R139 L140
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0045182 translation regulator activity
GO:0048027 mRNA 5'-UTR binding
Biological Process
GO:0000028 ribosomal small subunit assembly
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0006417 regulation of translation
GO:0030218 erythrocyte differentiation
GO:0030490 maturation of SSU-rRNA
GO:0042274 ribosomal small subunit biogenesis
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:0014069 postsynaptic density
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

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6ip6, PDBe:6ip6, PDBj:6ip6
PDBsum6ip6
PubMed31080011
UniProtP62263|RS14_HUMAN Small ribosomal subunit protein uS11 (Gene Name=RPS14)

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