Structure of PDB 8pvk Chain LK Binding Site BS01

Receptor Information
>8pvk Chain LK (length=158) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NEIKIIHLRATGGEVGASSALAPKIGPLGLSPKKVGEDIAKATADWKGLR
VTVRLTIQNRQAQVSVVPTASALIIRALKEPPRDRKKEKNIKHNKSVSLD
EIIEIARTMRFKSFSKDLKGGVKEILGTAFSVGCQVDGKSPKAISDAIEA
GEIDIPDE
Ligand information
>8pvk Chain C1 (length=3138) [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
ucuaguuugacauugugaaaagacauaggagguguagaauaggugggagc
uucggcgccagugaaauaccacuacuccuauuguuuuuuuacuuauucaa
ugaagcggggcuggacuugcguccaacuucuggaguuaagguccuucgcg
ggccgacccggguugaagacauugucagguggggaguuuggcuggggcgg
cacaucugugcagguguccuaaggggggcucauggagaacagaaaucucc
aguagaacaaaaggguaaaaguccccuugauuuugauuuucagugugaau
acaaaccaugaaaguguggccuaucgauccuuuagucccucgaaauuuga
ggcuagaggugccagaaaaguuaccacagggauggcuuguggcggccaag
cguucauagcgacgucgcuuugauccuucgaugucggcucuuccuaucau
accgaagcagaauucgguaagcguuggauuguucacccacuaauagggaa
cgugagcuggguuuagaccgucgugagacagguuaguuuuacccuacuga
ugaacucgucgcaaugguaauucagcuuaguacgagaggaaccgcugauu
cagauaauugguuuuugcgguuguccgaccgggcagugccgcgaagcuac
caucugcuggauaauggcugaacgccucuaagucagaauccaugccagaa
cgcgacgauacuacccgcacguuguagacguauaagaauaggcuccggcc
ucguauccuagcaggcgauuccuccgccggccucgaaguggccgucggua
auucgcguauugcaauuuagacacgcgcgggaucaaauccuuugcagacg
acuuagaugugcgaaaggguccuguaagcaguagaguagccuuguuguua
cgaucugcugaggguaagcccuccuucgccuagauuuc
...........................<<<<<<.....<...<..>....
..>>>>>.>.........<<....>>..<<<<<......<<.>...>>..
...>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>.
...<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.(
(......<<<.....))>>>.>..>>..>>.>>>>..>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..((
((((>>>>>..>>>..................................<<
....>>...............<<<<....>>>>.................
.................<<<<.<<<<<<.<...<<.<<<<<<<<<.....
<<<<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<
<<<<<<<<.......<<<<<<<<......<<<<<....>>>>>.......
>>>>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>
>>>>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<
<<<<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>
>.......<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>
>...>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<
<..<<.<<........>>>>.>>>....>>>>>>>>>...<<.......>
>......>>>>>>......>.>>...<<<<<......<<<....>>>..<
<<<<<<<<.....<<.<<<<<<<.....<<<........>>.>.....>>
>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>...>>>>>
>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>..
.<<<<<<<...<<<(((.....<<<<<<......<..........<<<.<
<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>...
......<<......>>...>>>>>...>>>>>>>>>>>>>..........
))).>....>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>
>>>>>>....>>>>>.<.<<<<<<<<.<<......<<<<.<<<<....>>
>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<<.....<<<
<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<...
..>>.>>>>>>....((<<<<<<...<<<<..<<<....>>>........
<<<<<......>>>>>...>>>>....>>...<<<<<........>>>>>
))<<<<.<<<<.<<<....<<<....>>>...<.((<<<<<<...<<<<.
<<<<<<<.<<<<<.<<<<...[[..>>>>.><...<<<<<....<<<<<<
....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<...
...>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>...>..
...>>>...>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<.....<<<<<<<.<<..............
.<<<<<....<<..>>.....>>>>><<.<<<<<<<<<<<.<<<<<..>>
>>>......>>>>>..>>>>>>.>>............<<<<<<<<<..<<
<.........>>>..<<<<<<<....<<<<.....>>>>......>>>>>
>>.........<<.<<<<<<....<<<.....<<<<....>>>>.....>
>>.>>>>..>>>>.<<<<<<.......>>>>>>......<<..>>.....
.>>.>>>>>>>.....>>.>>>>>>>..>>>>>>....>>....<<<<<.
.......>>>>>....<<<<<..<<<........<<<<<.<<<<<<..<<
<<<.<<<<<<<<..<<<<<<<<<<<<<<<<<..........<<<<<..<<
....>>............>>>>>.>>>>>>>.>>>>>>>>>>...<<<<<
.....<<<<..<<<<<....>>>>>..........))..<<<<<.....>
>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>.......<<<<<<
.<<<<<<<..>>>>>>>>>...<<<<<<<...<<<<<<.......>>>>>
>.....<<......>>....>>>>>>>....<<<<.<.<<<.....>>>.
>>>>><<<<....>>>.>>>>>.<<...<<<<<<<..<<<<.))))))>>
>>>>>>>>>.....>>..>>>>..>>>>>>>.........<<<<<<...<
<.......>>...>>>>>>...............<<<<...<<<<..<.<
<<<<<<......>>>>>>>...>.<<<.........>>>.....>>>>..
.....>>>>......<<<<<<<....>>>.>>>>........>>>.>>>>
>....<<<<<<<..<<<<.<.<<<<<.................>>>>>.>
<<<<<...<<<<....<<<<<<<<<<]]..>>>>>..>>>>>...>>>>.
.>>>>>.<<<<...<<<<<...........>>>>>...>>>>.>>>>...
.>>>>>>>.....<<<<<.<<.<<<......<<.......<<<<..>>>>
....>>........<<<<.....<<<.<<<<<.......>>>>>.>>>..
..>>>>..............>>>>>.>>>>>...<<<<<<<.........
....>>....<<<<<<<<<.<<<....<<<<....<<<<<......>>>>
>...>>>>...>>>....>>>>..>>>>>...>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pvk Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Resolution2.55 Å
Binding residue
(original residue number in PDB)
R16 T76 S78 K96 N97 H100 M116 K119 S122 K130 E131 G134 T135 F137 S138 K149
Binding residue
(residue number reindexed from 1)
R9 T69 S71 K89 N90 H93 M109 K112 S115 K123 E124 G127 T128 F130 S131 K142
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003735 structural constituent of ribosome
GO:0070180 large ribosomal subunit rRNA binding
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
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:8pvk, PDBe:8pvk, PDBj:8pvk
PDBsum8pvk
PubMed37921038
UniProtG0SGH8

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