Structure of PDB 8pv5 Chain Lh Binding Site BS01

Receptor Information

>8pv5 Chain Lh (length=118) Species: 759272 (Thermochaetoides thermophila DSM 1495)

NGKVKAGQLWSKNKEELTKILGELKTELSQLRIQKIAKLNKIHDLRKSIA
RVLTVINAKQRAQLRLFYKNKKYLPLDLRPKLTRALRRRLSKEDASRVLE
KTKKRLTHFPQRKYAVKA

Ligand information

>8pv5 Chain C1 (length=3060)

uugaccucggaucagguaggaggacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaacagggauugcccuaguaacggcgagugaagc
ggcaacagcucaaauuugaaagcuggcuucggcccgcguuguaauuugga
gaggaugcuuugggcgaggcuccuucugaguucccuggaacgggacgcca
cagagggugagagccccguauaguuggaagccaagccuguguaaagcucc
uucgacgagucgaguaguuugggaaugcugcucaaaaugggagguaaauu
ucuucuaaagcuaaauaccggccagagaccgauagcgcacaaguagagug
aucgaaagaugaaaagcacuuugaaaagaggguuaaauagcacgugaaau
uguugaaagggaagcgcuugugaccagacuugcgcccggcggaucauccg
guguucucaccggugcacuccgccgggcucaggccagcaucgguucuggc
ggggggauaaaggcccagggaauguggcuccuccgggaguguuauagccc
uggguguaauacccucgccgggaccgaggaccgcgcucugcaaggaugcu
ggcguaauggucaccagcgacccgucuugaaacacggaccaaggagucaa
gguuuugcgcgaguguuuggguguaaaacccgcacgcguaaugaaaguga
acguaggugagagcuucggcgcaucaucgaccgauccugauguauucgga
uggauuugaguaggagcguuaagccuuggacccgaaagauggugaacuau
gcuuggauagggugaagccagaggaaacucugguggaggcucgcagcggu
ucugacgugcaaaucgaucgucaaaucugagcaugggggcgaaagacuaa
ucgaaccaucuaguagcugguuaccgccgaaguuucccucaggauagcag
ugucgaccuucaguuuuaugagguaaagcgaaugaacuuuaaauauguaa
gaagcccuuguuacuuaacugaacgugggcauucgaauguaucgacacua
gugggccauuuuugguaagcagaacuggcgaugcgggaugaaccgaacgc
gggguuaaggugccggaguggacgcucaucagacaccacaaaaggcguua
guacaucuugacagcaggacgguggccauggaagucggaauccgcuaagg
acuguguaacaacucaccugccgaauguacuagcccugaaaauggauggc
gcucaagcgucccacccauaccccgcccucaggguagaaacgaugcccug
aggaguaggcggccguggaggucagugacgaagccuagggcgugagcccg
ggucgaacggccucuagugcagaucuuggugguaguagcaaauacuucaa
ugagaacuugaaggaccgaaguggggaaagguuccaugugaacagcgguu
ggacauggguuagucgauccuaagccauagggaaguuccguuucaaaggg
gcacucgugccccguguggcgaaagggaagccgguuaauauuccggcacc
uggauguggguuuugcgcggcaacgcaacugaacgcggagacgacggcgg
gggccccgggcagaguucucuuuucuucuuaacggucuaucacccuggaa
acaguuugucuggagauaggguuuaauggccggaagagcccgacacuucu
gucggguccggugcgcucucgacgucccuugaaaauccgcgggagggaau
aauucucacgccaggucguacucauaaccgcagcagguccccaaggugaa
cagccucugguugauagaacaauguagauaagggaagucggcaaaauaga
uccguaacuucgggaaaaggauuggcucuaaggguugguaacaaccaacu
uagaacugguacggacagggggaaucugacugucuaauuaaaacauagca
uugcgauggccagaaagugguguugacgcaaugugauuucugcccagugc
ucugaaugucaaagugaagaaauucaaccaagcgcggguaaacggcggga
guaacuaugacucucuguagccaaauggauuaacgagauucccacugucc
cuaucuacuaucuagcgaaaccacagccaagggaacgggcuuggcaaaau
cagcggggaaagaagacccuguugagcuugacucuaguuugacauuguga
aaagauuuuuuuacuuauucaaugaagcggggcuggacuugcguccaacu
ucuggaguuaagguccuucgcgggccgacccggguugaagacauugucag
guggggaguuuggcuggggcggcacaucugugcagguguccuaagggggg
cucauggagaacagaaaucuccaguagaacaaaaggguaaaaguccccuu
gauuuugauuuucagugugaauacaaaccaugaaaguguggccuaucgau
ccuuuagucccucgaaauuugaggcuagaggugccagaaaaguuaccaca
gggauggcuuguggcggccaagcguucauagcgacgucgcuuugauccuu
cgaugucggcucuuccuaucauaccgaagcagaauucgguaagcguugga
uuguucacccacuaauagggaacgugagcuggguuuagaccgucgugaga
cagguuaguuuuacccuacugaugaacucgucgcaaugguaauucagcuu
aguacgagaggaaccgcugauucagauaauugguuuuugcgguuguccga
ccgggcagugccgcgaagcuaccaucugcuggauaauggcugaacgccuc
uaagucagaauccaugccagaacgcgacgauacuacccgcacguuguaga
cguauaagaauaggcuccggccucguauccuagcaggcgauuccuccgcc
ggccucgaaguggccgucgguaauucgcguauugcaauuuagacacgcgc
gggaucaaauccuuugcagacgacuuagaugugcgaaaggguccuguaag
caguagaguagccuuguuguuacgaucugcugaggguaagcccuccuucg
ccuagauuuc

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pv5 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
• Resolution: 2.86 Å
• Binding residue (original residue number in PDB): K79 Y80 R86 R91 R95 E107 K108 K111 R112 T114 H115 K120
• Binding residue (residue number reindexed from 1): K72 Y73 R79 R84 R88 E100 K101 K104 R105 T107 H108 K113

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:8pv5, PDBe:8pv5, PDBj:8pv5
• PDBsum: 8pv5
• PubMed: 37921038
• UniProt: G0S0D7