Structure of PDB 8ipb Chain NB Binding Site BS01

Receptor Information
>8ipb Chain NB (length=68) Species: 4565 (Triticum aestivum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PKQIHEIKDFLLTARRKDARSVRIKRTKDAVKFKVRCSRYLYTLCVFDAD
KANKLKQSLPPGLSVQEV
Ligand information
>8ipb Chain RB (length=3147) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gcgcgaccccaggucaggcgggacuaccgcugaguuuaagcauauaaaua
agcggaggagaagaaacuuacaaggauuccccuaguaacggcgagcgaac
cgggagcagcccagcuugagaaucgggcggcugugccguccgaauuguag
ucuggagaggcguccucagcgacggaccgggcccaaguccccuggaaagg
ggcgccugggagggugagagccccguccggcccggacccugucgccccac
gaggcgccgucaacgagucggguuguuugggaaugcagcccaaaucgggc
gguagacuccguccaaggcuaaauacaggcgagagaccgauagcgaacaa
guaccgcgagggaaagaugaaaaggacuuugaaaagagagucaaagagug
cuugaaauugccgggagggaagcggaugggggccggcgaugcgccccggc
gcucggggcguggacuguugucggccgcgccggcggccaaagcccggggg
cuccgcgcccccggcagccgucgucggcacggccgguacccgcgcgccga
aaggcgugccccucggggcacugcgcugcaacgcccugcgggcucuccau
ccgacccgucuugaaacacggaccaaggagucugacaugcgugcgagucg
acggguucugaaaccugggaugcgcaaggaagcugacgagcgggaggccc
ucacgggccgcaccgcuggccgacccugaucuucugugaaggguucgagu
uggagcacgccugucgggacccgaaagauggugaacuaugccugagcggg
gcgaagccagaggaaacucugguggaggcucgaagcgauacugacgugca
aaucguucgucugacuuggguauaggggcgaaagacuaaucgaaccaucu
aguagcugguucccuccgaaguuucccucaggauagcuggagcccauuac
gaguucuaucagguaaagccaaugauuagaggcauuggggacgcaacguc
cucgaccuauucucaaacuuuaaauagguaggauggcgcggcugcuucgg
ugagccgugccauggaaucgggugcuccaagugggccauuuuugguaagc
agaacuggcgaugcgggaugaaccggaagccggguuacggugcccaacug
cgcgcuaaccuagaacccacaaaggguguuggucgauuaagacagcagga
cgguggucauggaagucgaaauccgcuaaggaguguguaacaacucaccu
gccgaaucaacuagccccgaaaauggauggcgcugaagcgcgcgacccac
acccggccaucugggcgagugccaugccccgaugaguaggagggcgcggc
ggccgaugcaaaacccggggcgcgagcccgggcggagcggccgucggugc
agaucuuggugguaguagcaaauauucaaaugagaacuuugaaggccgaa
gaggagaaagguuccaugugaacggcacuugcacauggguaagccgaucc
uaagggaagggguaaccccggcagauagcgcgaucacgcgcauccccgaa
agggaaucggguuaagauuucccgagccgggauguggcgguugacggcga
cguuaggaaguccggagacgccggcgggggccucgggaagaguuaucuuu
ucugcuuaacggccugccaacccuggaaacgguucagccggagguagggu
ccaguggccggaagagcacacgucgcgcgguguccggugcgcccccggcg
gcccaugaaaauccggaggaccgaguaccguucacgcccggucguacuca
uaaccgcaucaggucuccaaggugaacagccucuggccaauggaacaaug
uaggcaagggaagucggcaaaacggauccguaacuucgggaaaaggauug
gcucugaggacugacagucgacucagaacugguacggacaaggggaaucc
gacuguuuaauuaaaacaaagcauugcgaugguccucgcggaugcugacg
caaugugauuucugcccagugcucugaaugucaaagugaagaaauucaac
caagcgcggguaaacggcgggaguaacuaugacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaaugaauuaacgagauucc
cacugucccugucuacuauccagcgaaaccacagccaagggaacgggcuu
ggcggaaucagcggggaaagaagacccuguugagcuugacucuaguccga
cuuugugaaaugaauuuuacuuauuccgugggucggaagcggggcaugcc
ccuccuuuuggcuccaaggcccggucuuaccgggccgauccgggcggaag
acauugucagguggggaguuuggcuggggcggccaaucuguuaaaagaua
acgcagguguccuaagaugagcucaacgagaacagaaaucucguguggaa
caaaaggguaaaagcucguuugauucugauuuccaguacgaauacgaacc
gugaaagcguggccuaucgauccuuuagaucuucggaguuugaagcuaga
ggugucagaaaaguuaccacagggauuacuggcuuguggcagccaagcgu
ucauagcgacguugcuuuuugauccuucgaugucggcucuuccuaucauu
gcgaagcagaauucaccaaguguuggauuguucacccaccaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gacagugucgcgauaguaauucaaccuaguacgagaggaaccguugauuc
acacaauuggucaucgcgcuugguugaaaagccaguggcgcgaagcuacc
gugugccggauuaugacugaacgccucuaagucagaauccaagcuagcau
gcgacgccugcgcccgccgcccgccccgacccacguuaggggcgcuugcg
cccccaagggcccgugccauuggcuaagccgguccggccgaagugccgcg
gucggccgccucgaagcucccuucccaacgggcggugggcugaauccuuu
gcagacgacuuaaauacgcgacggggcauuguaaguggcagaguggccuu
gcugccacgauccacugagauccaguccccgggucgcacggauucgu
..........................<<<<<.....<......>......
>>>>>...........<<....>>..<<<<<.......<.....>.....
.>>>>>..[[[....<......<<<<<<<<<...>>>>>>>>>......>
......<<<<<<.<<<<.<<<<<<<.<<<<<<<.....<<<<......>>
>>.((......<<<.....))>>>....>>>>>>>...>>>>>>>.....
>>>>>>>>.>>........<<<<<<<........>>>>>>>.....((((
(..<<<<<<)))))..]]]...............................
...<<....>>...............<<<<....>>>>............
......................<<<<<<<<<<<<......<<<<<<<<..
...>>>>>>>>.<..<<<<<<<<<<<<.<<<<<<<<<......<<<<<<<
.......>>>>>>>.....>>>>>>>>>.>>>>>>>.....<<<<<<<..
..>>>.<<<<<<..>>>>>>..>>>>..>>>>>..>....>>>.>>>>>>
>>>..<<<<........>>>><<<<<<....<<<<<<.<<<<<<..<<..
..<<<<......>>>>.....>>...<<....>>....<<<<<..<<<<<
....>>>>>...>>>>>.<<<<<<<.....<....>.....>>.>>>.>>
....>>>>>>.>>>>>>..<<.<...<<<<<<.....<<<<<<<<<..<<
<....<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<......
..>>>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>.
.....>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<....<
<<.<<<<<<<.....<<<....<<<....<<<.....<<<<.......>>
>>...>>>....>>>..>.>>.....>>>>>...<<<<<<<<<.<.....
.>>>>>>>>>>....>>>>>>>.>>>>>>.>>..<<<<.<<<<<.....>
>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((.....<
<<<<<.......<..........<<<.<<<<<<.<<<.......<<<...
<<.....<.........>.....>>........................>
>>...>>>.>>>>>>>>>..........))).>....>>>>>>.>>>...
>>>>>>><<<<.<<<<.........>>>>.>>>>....>>>>>><.<<<<
<<<<<........<<<.<<<<....>>>>>>>.....>>>>>>>>>..>.
....>>>>>><<.....<<.....<<<<<<.......>>>>>><<<<...
..<<<<<.<<...<<<<<<...<<.....>>.>>>>>>....((<<<<<<
...<<<...<<<....>>>.........<<<<....>>>>....>>>...
.>>...<<<<<.........>>>>>))<<<<.<<<<<<<<...<<<....
>>>...<...<<<<<<...<<<<.<<<<<<<.<<<<<.<<<<.......>
>>>.><...<<<<<.....<<<<<<....<<<<...>>>>....>>>>>>
.....>>>>>....><<<<..........>>>>>>>>...>>>>>>>.>>
>>.........>>>>>>...>......>>>>.>>>>>>>>>>>>..>>..
...<<......>>>>>>>.<<<<.....>>>>..>>>>..<<<<.....<
<<<<<<.<<.........<.....<<<<<...............>>>>><
<.<<<<<<<<<<<.>>>>>..>>>>>>.>>............<<<<<<<<
<..<<<.........>>>..<<<<<<<....<<<<....>>>>......>
>>>>>>...<<<.<<<..<<<<<<.....<<.....<<<<....>>>>..
...>>..>>>>..>>>>><<<<<<.......>>>>>>........<....
.......<<<<<.......>>>>>.....>....>>>....>>.>>>>>>
>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<........>>>
>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<.<<<.<<
<...<<<<<<<..>>>>>>>...<<<<<.....<<<<...<<<<....>>
>>...............<<<<<<<.....>>>>>>>..>>>>..>>>>>.
.....>>>.>>>..>>>>>...<<<.....>>>..<<<<<<.........
..>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<
<...(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<
<<....>>>.>>))).......((((((..((((.>>>>>>)))))))))
)..........]]]]..}}]]]].......<<.<...<<<<<<...<<..
.....>>...>>>>>>....>.>.>.......<<<<<.<<<<<<..<<<.
<.<<<......>>>.>...>>>.<<<.........>>>.....>>>>>..
>...>>>.>>....<<<<<<<....>>>.>>>>....}}..}}}.]]]]]
....<<<<<<<..<<<<.<.<<<<<.................>>>>>.><
<<<<...<<<<....<<<<<<<<<......>>>>..>>>>>...>>>>..
>>>>>..<<<...<<<<<...........>>>>>...>>>..>>>>....
>>>>>>>....<<<<<<<<<<<<......<<.......<<<<<<<..>>>
>>>>....>>...........<<<...<<<<<<<<<<<......>>>>.>
>>>>>>.>>>..................>>>>>>>>>>>>.<<<<<<<..
...........>.....<<<<<<<<<.<<<....<<<<....<<<<<...
...>>>>>...>>>>...>>>....>>>>...>>>>>..>>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8ipb Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Resolution3.4 Å
Binding residue
(original residue number in PDB)
P2 K3 Q4 R17 D19 K26 K33 K35 R37 S39 R40 Y41 L42
Binding residue
(residue number reindexed from 1)
P1 K2 Q3 R16 D18 K25 K32 K34 R36 S38 R39 Y40 L41
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
GO:0022618 protein-RNA complex assembly
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8ipb, PDBe:8ipb, PDBj:8ipb
PDBsum8ipb
PubMed38267667
UniProtA0A1D5W6Q2

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