Structure of PDB 8pvl Chain Lh Binding Site BS01

Receptor Information
>8pvl Chain Lh (length=122) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGKVKAGQLWSKNKEELTKILGELKTELSQLRIQKISSSGAKLNKIHDLR
KSIARVLTVINAKQRAQLRLFYKNKKYLPLDLRPKLTRALRRRLSKEDAS
RVLEKTKKRLTHFPQRKYAVKA
Ligand information
>8pvl Chain C1 (length=3078) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agguugaccucggaucagguaggaggacccgcugaacuuaagcauaucaa
uaagcggaggaaaagaaaccaacagggauugcccuaguaacggcgaguga
agcggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuu
ggagaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacg
ccacagagggugagagccccguauaguuggaagccaagccuguguaaagc
uccuucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaa
auuucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguaga
gugaucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacguga
aauuguugaaagggaagcgcuugugaccagacuugcgcccggcggaucau
ccgguguucucaccggugcacuccgccgggcucaggccagcaucgguucu
ggcggggggauaaaggcccagggaauguggcuccuccgggaguguuauag
cccuggguguaauacccucgccgggaccgaggaccgcgcucugcaaggau
gcuggcguaauggucaccagcgacccgucuugaaacacggaccaaggagu
caagguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaag
ugaacguaggugagagcuucggcgcaucaucgaccgauccugauguauuc
ggauggauuugaguaggagcguuaagccuuggacccgaaagauggugaac
uaugcuuggauagggugaagccagaggaaacucugguggaggcucgcagc
gguucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagac
uaaucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauag
cagugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauaug
uaagaagcccuuguuacuuaacugaacgugggcauucgaauguaucgaca
cuagugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaa
cgcgggguuaaggugccggaguggacgcucaucagacaccacaaaaggcg
uuaguacaucuugacagcaggacgguggccauggaagucggaauccgcua
aggacuguguaacaacucaccugccgaauguacuagcccugaaaauggau
ggcgcucaagcgucccacccauaccccgcccucaggguagaaacgaugcc
cugaggaguaggcggccguggaggucagugacgaagccuagggcgugagc
ccgggucgaacggccucuagugcagaucuuggugguaguagcaaauacuu
caaugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcg
guuggacauggguuagucgauccuaagccauagggaaguuccguuucaaa
ggggcacucgugccccguguggcgaaagggaagccgguuaauauuccggc
accuggauguggguuuugcgcggcaacgcaacugaacgcggagacgacgg
cgggggccccgggcagaguucucuuuucuucuuaacggucuaucacccug
gaaacaguuugucuggagauaggguuuaauggccggaagagcccgacacu
ucugucggguccggugcgcucucgacgucccuugaaaauccgcgggaggg
aauaauucucacgccaggucguacucauaaccgcagcagguccccaaggu
gaacagccucugguugauagaacaauguagauaagggaagucggcaaaau
agauccguaacuucgggaaaaggauuggcucuaaggguugggcacgugcg
ugcgguuaacaaccaacuuagaacugguacggacagggggaaucugacug
ucuaauuaaaacauagcauugcgauggccagaaagugguguugacgcaau
gugauuucugcccagugcucugaaugucaaagugaagaaauucaaccaag
cgcggguaaacggcgggaguaacuaugacucucuguagccaaauggauua
acgagauucccacugucccuaucuacuaucuagcgaaaccacagccaagg
gaacgggcuuggcaaaaucagcggggaaagaagacccuguugagcuugac
ucuaguuugacauugugaaaagauuuuuuuacuuauucaaugaagcgggg
cuggacuugcguccaacuucuggaguuaagguccuucgcgggccgacccg
gguugaagacauugucagguggggaguuuggcuggggcggcacaucugug
cagguguccuaaggggggcucauggagaacagaaaucuccaguagaacaa
aaggguaaaaguccccuugauuuugauuuucagugugaauacaaaccaug
aaaguguggccuaucgauccuuuagucccucgaaauuugaggcuagaggu
gccagaaaaguuaccacagggauggcuuguggcggccaagcguucauagc
gacgucgcuuugauccuucgaugucggcucuuccuaucauaccgaagcag
aauucgguaagcguuggauuguucacccacuaauagggaacgugagcugg
guuuagaccgucgugagacagguuaguuuuacccuacugaugaacucguc
gcaaugguaauucagcuuaguacgagaggaaccgcugauucagauaauug
guuuuugcgguuguccgaccgggcagugccgcgaagcuaccaucugcugg
auaauggcugaacgccucuaagucagaauccaugccagaacgcgacgaua
cuacccgcacguuguagacguauaagaauaggcuccggccucguauccua
gcaggcgauuccuccgccggccucgaaguggccgucgguaauucgcguau
ugcaauuuagacacgcgcgggaucaaauccuuugcagacgacuuagaugu
gcgaaaggguccuguaagcaguagaguagccuuguuguuacgaucugcug
aggguaagcccuccuucgccuagauuuc
...........................<<<<<<.....<...<..>....
..>>>>>.>.........<<....>>..<<<<<......<<.>...>>..
...>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>.
...<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.(
(......<<<.....))>>>.>..>>..>>.>>>>..>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..((
((((>>>>>..>>>..................................<<
....>>...............<<<<....>>>>.................
.................<<<<.<<<<<<.<...<<.<<<<<<<<<.....
<<<<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<
<<<<<<<<.......<<<<<<<<......<<<<<....>>>>>.......
>>>>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>
>>>>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<
<<<<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>
>.......<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>
>...>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<
<<.<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>
>......>>>>>>......>.>>...<<<<<......<<<.{..>>>..<
<<<<<<<<.....<<.<<<<<<<.....<<<........>>.>.....>>
>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>...>>>>>
>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>..
.<<<<<<<...<<<(((.....<<<<<<......<..........<<<.<
<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>...
......<<......>>...>>>>>...>>>>>>>>>>>>>..........
))).>....>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>
>>>>>>....>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>
>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<<
<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<...
..>>.>>>>>>....((<<<<<<...<<<<..<<<....>>>........
<<<<<......>>>>>...>>>>....>>...<<<<<........>>>>>
))<<<<.<<<<.<<<....<<<....>>>...<...<<<<<<...<<<<.
<<<<<<<.<<<<<.<<<<...[[..>>>>.><...<<<<<....<<<<<<
....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<...
...>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>...>..
...>>>...>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<.....<<<<<<<.<<.........<....
.<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.<<<<<..>>
>>>......>>>>>..>>>>>>.>>............<<<<<<<<<..<<
<.........>>>..<<<<<<<....<<<<.....>>>>......>>>>>
>>.........<<.<<<<<<....<<<.....<<<<....>>>>.....>
>>.>>>>..>>>>.<<<<<<.......>>>>>>......<<..>>.....
.>>.>>>>>>>..>..>>.>>>>>>>..>>>>>>....>>....<<<<<.
.......>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<
<<<.<<<<<<<<..<<<<<<<<..>>>>>>>>...<<<<<.....<<<<.
.<<<<<....>>>>>..............<<<<<.....>>>>>..>>>>
..>>>>>.....>>>>>>>>..>>>>>..}....<<<<<<.<<<<<<...
.>>>>>>>>...<<<<<<<...<<<<<<.......>>>>>>.....<<..
....>>....>>>>>>>....<<<<...<<<.....>>>..>>>>.<<<.
...>>>..>>>>.<<...<<<<<<<..<<<<.))))))>>>>>>>>>>>.
....>>..>>>>..>>>>>>>.........<<<<<<...<<.......>>
...>>>>>>...............<<<<..<<<<<..<.<<<<<<<....
..>>>>>>>...>.<<<.........>>>.....>>>>>......>>>>.
.....<<<<<<<....>>>.>>>>........>>>.>>>>>....<<<<<
<<..<<<<.<.<<<<<.................>>>>>.><<<<<...<<
<<....<<<<<<<<<<]]..>>>>>..>>>>>...>>>>..>>>>>.<<<
<...<<<<<...........>>>>>...>>>>.>>>>....>>>>>>>..
...<<<<<.<<.<<<......<<.......<<<<..>>>>....>>....
....<<<<.....<<<.<<<<<.......>>>>>.>>>....>>>>....
..........>>>>>.>>>>>...<<<<<<<.............>>....
<<<<<<<<<.<<<....<<<<....<<<<<......>>>>>...>>>>..
.>>>....>>>>..>>>>>...>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pvl Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Resolution2.19 Å
Binding residue
(original residue number in PDB)
K79 Y80 R86 R91 R95 K108 K111 R112 H115 F116
Binding residue
(residue number reindexed from 1)
K76 Y77 R83 R88 R92 K105 K108 R109 H112 F113
Enzymatic activity
Enzyme Commision number 2.4.99.18: dolichyl-diphosphooligosaccharide--protein glycotransferase.
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0004576 oligosaccharyl transferase activity
GO:0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity
GO:0016757 glycosyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006486 protein glycosylation
GO:0018279 protein N-linked glycosylation via asparagine
GO:0043687 post-translational protein modification
Cellular Component
GO:0005840 ribosome
GO:0016020 membrane
GO:1990904 ribonucleoprotein complex

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Molecular Function

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Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8pvl, PDBe:8pvl, PDBj:8pvl
PDBsum8pvl
PubMed37921038
UniProtG0S0D7

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