Structure of PDB 6p5n Chain g Binding Site BS01

Receptor Information

>6p5n Chain g (length=68) Species: 9986 (Oryctolagus cuniculus)

KSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFM
ASHFDRHYCGKCCLTYCF

Ligand information

>6p5n Chain 2 (length=1697)

uaccugguugauccugccaguagcauaugcuugucucaaagauuaagcca
ugcaugucuaaguacgcacggccgguacagugaaacugcgaauggcucau
uaaaucaguuaugguuccuuuggucgcucgacuuggauaacugugguaau
ucuagagcuaauacaugccgacgggcgcugacccccuucgcgggggggau
gcgugcauuuaucaguggugacucuagauaaccucgggccgaucgcacgc
ccggcggcgacgacccauucgaacgucugcccuaucaacuuucgauggua
gucgccgugccuaccauggugaccacgggugacggggaaucaggguucga
uuccggagagggagccugagaaacggcuaccacauccaaggaaggcagca
ggcgcgcaaauuacccacucccgacccggggagguagugacgaaaaauaa
caauacaggacucuuucgaggcccuguaauuggaaugaguccacuuuaaa
uccuuuaacgaggauccauuggagggcaagucuggugccagcagccgcgg
uaauuccagcuccaauagcguauauuaaaguugcugcaguuaaaaagcuc
guaguuggaucuugggagcggccguccccugcucggcgccggcccgaagc
guuuacuuugaaaaaauuagaguguucaaagcaggccgccuggauaccgc
agcuaggaauaauggaauaggaccgcgguucuauuuuguugguuuucgga
acugaggccaugauuaagagggacggccgggggcauucguauugcgccgc
uagaggugaaauucuuggaccggcgcaagacggaccagagcgaaagcauu
ugccaagaauguuuucauuaaucaagaacgaaagucggagguucgaagac
gaucagauaccgucguaguuccgaccauaaacgaugccgaccggcgaugc
ggcggcguuauucccaugacccgccgggcagcuuccgggaaaccaaaguc
uuuggguuccggggggaguaugguugcaaagcugaaacuuaaaggaauug
acggaagggcaccaccaggaguggagccugcggcuuaauuugacucaaca
cgggaaaccucacccggcccggacacggacaggauugacagauugauagc
ucuuucucgauuccgugggugguggugcauggccguucuuaguuggugga
gcgauuugucugguuaauuccgauaacgaacgagacucuggcaugcuaac
uaguuacgcgaccccggucggcguaacuucuuagagggacaaguggcguu
cagccacccgagauugagcaauaacaggucugugaugcccuuagaugucc
ggggcugcacgcgcgcuacacugacuggcucagcgugugccuacccuacg
ccggcaggcgcggguaacccguugaaccccauucgugauggggaucgggg
auugcaauuauuccccaugaacgaggaauucccaguaagugcgggucaua
agcuugcguugauuaagucccugcccuuuguacacaccgcccgucgcuac
uaccgauuggaugguuuagugaggcccucggaucggccccgccggggugc
ccuggcggagcgcugagaagacggucgaacuugacuaucuagaggaagua
aaagucguaacaagguuuccguaggugaaccugcggaaggaucauua

...<<<<<.[.((((>>>>><<<.<<<<<<...<.<<..<......<<<.
<<<...<....<<....<<..........>>...>>.>.......<<...
.....<<<.<....<<....<<<<<........<<.....<<.<<<....
.>>>.>>......>>.........<<<<...<<<<<<....>>>>>>...
>>>>...<<..<....<......>...>.>>...........<<<<.<<<
<.>>>>>>>>.>>.>>>...>>..>.>>>.<<<....<<<....<<<<<<
<.........>>>>>>>>>>......>>>...<<<.<<<<....>>>>..
..>>>.>>.<<.<<<..........>>>.>>.<.<<....>>.>...>>>
>>>.........<<<....<<<<...>>>>..>>>..>...>>.>.....
<<<.<<<...<<<....>>>....>>>..>>>......<<..<.......
....>..>>.........<<<<<((......<<<<.....<<..))>>..
.....>>>>.>>>>>..>>>>>>.>>>.........<.<((.....<.<<
...<<<.<<......<.<<<..>>>..>.<<.<<<<.<<..>>>>>>..>
>.<<<<<<.<.......<<...<.......>.<<<<.>>>>...>>....
..>.>>>..>>>..........<<.<<<<<<<...............>>>
>>>>.>>......>>....<<<<<<......<<<<..<<..<<<<<<<<.
..<<<......>>>......>>>>>>>.>.>>.......<<....>>...
>>>>.....>>>.>>>...>>>...>>.>....<<<<<<<...<...<<<
<.<.....>.>>>>...>>>>>>>>..........<<<.<<.<<<..<.<
<<<<<.<<<<......>>>>>>>>>>.>..>>>...<<..))>>...>>.
....>>>.>.>.<<<......<<<<....>>>>....>>>..)))).]<<
<<<.<<<<<<<..<<..<<<<<..<<<.<<<<........<<........
>>..........<<<<<.<....<.<..........<...<<........
>>...>........>.>...<<.<<<..<<.<<<<<<....<<<.<<<<<
....>>>...<<<......>>>...>>.>>>....<<<.......<<<<.
.<<<<<<<<<<<....>>>.>>>>>>>>..>>>>........<<<<<...
..>>>>>........>>>....>>>.>>>.....>>>>>>>.....>.>>
>>>......>>>>.>>>.....<<.<<<........<.......<<<.<<
<<....>>>>.>>>....>.........>>>.>>......<.....<<<<
<..........>>>>>.....>.....>>>>>.....<<<<<<<<.....
..>>>>>>>>......>>...>>>>>>>>>>.>>....<..<<.<..<<<
<.<<....<<<<<<<<.<<<..<<<<.<<...<<<<<.<<<<<<<<....
>>>>>>>>...>>>>>...>>.>>>>..>>>.>>>>>>>>...>>.>>>>
...>.>>...>.....<<<<<<<<<<..>>>>>>>>>>.........

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6p5n The Israeli acute paralysis virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): K83 Y85 P88 K90 N91 K92 H93 K94 R95 K96 K99 L100 Y105 R118 F131 A133 S134 H135 F136 D137 R138 Y140 G142 T147
• Binding residue (residue number reindexed from 1): K1 Y3 P6 K8 N9 K10 H11 K12 R13 K14 K17 L18 Y23 R36 F49 A51 S52 H53 F54 D55 R56 Y58 G60 T65

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0031386 protein tag activity
• GO:0031625 ubiquitin protein ligase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0006412 translation
• GO:0016567 protein ubiquitination
• GO:0019941 modification-dependent protein catabolic process

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6p5n, PDBe:6p5n, PDBj:6p5n
• PDBsum: 6p5n
• PubMed: 31609474
• UniProt: G1SK22|RS27A_RABIT Ubiquitin-ribosomal protein eS31 fusion protein (Gene Name=RPS27A)