Structure of PDB 8pv8 Chain Lh Binding Site BS01

Receptor Information

>8pv8 Chain Lh (length=122) Species: 759272 (Thermochaetoides thermophila DSM 1495)

NGKVKAGQLWSKNKEELTKILGELKTELSQLRIQKISSSGAKLNKIHDLR
KSIARVLTVINAKQRAQLRLFYKNKKYLPLDLRPKLTRALRRRLSKEDAS
RVLEKTKKRLTHFPQRKYAVKA

Ligand information

>8pv8 Chain C1 (length=3085)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuuccggauagcaguguc
gaccuucaguuuuaugagagcgaaugauuagggacucgggggcgccuuca
uccauucucuguaagaagcccuuguuacuuaacugaacgugggcgaaugu
cgacacuagugggccauuuuugguaagcagaacuggcgaugcgggaugaa
ccgaacgcgggguuaaggugccggaguggacgcucaucagacaccacaaa
aggcguuaguacaucuugacagcaggacgguggccauggaagucggaauc
cgcuaaggacuguguaacaacucaccugccgaauguacuagcccugaaaa
uggauggcgcucaagcgucccacccauaccccgcccucaggguagaaacg
augcccugaggaguaggcggccguggaggucagugacgaagccuagggcg
ugagcccgggucgaacggccucuagugcagaucuuggugguaguagcaaa
uacuucaaugagaacuugaaggaccgaaguggggaaagguuccaugugaa
cagcgguuggacauggguuagucgauccuaagccauagggaaguuccguu
ucaaaggggcacucgugccccguguggcgaaagggaagccgguuaauauu
ccggcaccuggauguggguuuugcgcggcaacgcaacugaacgcggagac
gacggcgggggccccgggcagaguucucuuuucuucuuaacggucuauca
cccuggaaacaguuugucuggagauaggguuuaauggccggaagagcccg
acacuucugucggguccggugcgcucucgacgucccuugaaaauccgcgg
gagggaauaauucucacgccaggucguacucauaaccgcagcaggucccc
aaggugaacagccucugguugauagaacaauguagauaagggaagucggc
aaaauagauccguaacuucgggaaaaggauuggcucuaaggguugguaac
aaccaacuuagaacugguacggacagggggaaucugacugucuaauuaaa
acauagcauugcgauggccagaaagugguguugacgcaaugugauuucgc
ccagugcucuaugucaaagugaagaaauucaaccaagcgcggguaaacgg
cgggaguaacuaugacucucuuaagguuaacgagauucccacugucccua
ucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucag
cggggaaagaagacccuguugagcuugacucuaguuugacauugugaaaa
gacauaggagguguagaauaggugggagcuucggcgccagugaaauacca
cuacuccuauuguuuuuuuacuuauucaaugaagcggggcuggacuugcg
uccaacuucuggaguuaagguccuucgcgggccgacccggguugaagaca
uugucagguggggaguuugggcacaucugcagguguccuaaggggggcuc
auggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuugau
uuugauuuuugugaauacaaaccaugaaaguguggccccuuuagucccuc
gaaauuugaggcuagaggaaguuaccacagggauggcuuguggcggccaa
gcguucauagcgacgucgcuuugauccuucgaugucggcucuuccuauca
uaccgaagcagaauucgguaagcguuggauuguacccacuaauagggaac
gagcuggguuuagaccgucgugagacagguuaguuuuacccuacugauga
acucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauucag
auaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuaccau
cugcuggauaauggcugaacgccucuaagucagaauccaugccagaacgc
gacgauacuacccgcacguuguagacguauaagaauaggcuccggccucg
uauccuagcaggcgauuccuccgccggccucgaaguggccgucgguaauu
cgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacgacu
uagaugugcgaaaggguccuguaagcaguagaguagccuuguuguuacga
ucugcugaggguaagcccuccuucgccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv8 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.91 Å
• Binding residue (original residue number in PDB): K79 Y80 R86 R91 R95 E107 K108 K111 R112 T114 H115
• Binding residue (residue number reindexed from 1): K76 Y77 R83 R88 R92 E104 K105 K108 R109 T111 H112

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

External links

• PDB: RCSB:8pv8, PDBe:8pv8, PDBj:8pv8
• PDBsum: 8pv8
• PubMed: 37921038
• UniProt: G0S0D7