Structure of PDB 8pv3 Chain LY Binding Site BS01

Receptor Information
>8pv3 Chain LY (length=133) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVRPTVSSSRRKARKAHFSAPSSVRRVIMSAPLSKELREKYNVRSIPIR
KGDEVQIVRGAHKDKEGKVTSVYRLKYVIHVERVTREKATGQTVPIGIHP
SNVVITKLHLDKDRENILARIKAGREQVAKAKG
Ligand information
>8pv3 Chain C1 (length=2998) [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
gugauuucguagccaaauggauuaacgagauucccacugucccuaucuac
uaucuagcgaaaccacagccaagggaacgggcuuggcaaaaucagcgggg
aaagaagacccuguugagcuugacucuaguuugacauugugaaaauuuuu
acuuauucaaugaagcggggcuggacuugcguccaacuucuggaguuaag
guccuucgcgggccgacccggguugaagacauugucagguggggaguuug
gcuggggcggcacaucugugcagguguccuaaggggggcucauggagaac
agaaaucuccaguagaacaaaaggguaaaaguccccuugauuuugauuuu
cagugugaauacaaaccaugaaaguguggccuaucgauccuuuagucccu
cgaaauuugaggcuagaggugccagaaaaguuaccacagggauggcuugu
ggcggccaagcguucauagcgacgucgcuuugauccuucgaugucggcuc
uuccuaucauaccgaagcagaauucgguaagcguuggauuguucacccac
uaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuuu
acccuacugaugaacucgucgcaaugguaauucagcuuaguacgagagga
accgcugauucagauaauugguuuuugcgguuguccgaccgggcagugcc
gcgaagcuaccaucugcuggauaauggcugaacgccucuaagucagaauc
caugccagaacgcgacgauacuacccgcacguuguagacguauaagaaua
ggcuccggccucguauccuagcaggcgauuccuccgccggccucgaagug
gccgucgguaauucgcguauugcaauuuagacacgcgcgggaucaaaucc
uuugcagacgacuuagaugugcgaaaggguccuguaagcaguagaguagc
cuuguuguuacgaucugcugaggguaagcccuccuucgccuagauuuc
...........................<<<<<<.....<...<..>....
..>>>>>.>...[.....<<....>>..<<<<<......<<.>...>>..
...>>>>>..<<<..<<.......<<.<<<....>>>.>>.......>>.
...<<<<<.<<<<<<<<<..<<<<<<..<<<...<<<<......>>>>.(
(......<<<.....))>>>.>..>>..>>.>>>>..>>>>....>>>>>
>>>.>>........<<<<<<<........>>>>>>>.....<<<<<..((
((((>>>>>..>>>....].............................<<
....>>...............<<<<....>>>>.................
.................<<<<.<<<<<<.<...<<.<<<<<<<<<.....
<<<<<<....>>>>>>......>>>>>>>>>.>>.<<<<<<<.<<<<<<<
<<<<<<<<.......<<<<<<<<......<<<<<....>>>>>.......
>>>>>>>>......>>>>>>>>>>>>>>>........<<...>>.....>
>>>>>>....>>>>>>>.>>>>..<<<<.<....>.>>>><<<<<<...<
<<<<<<<<.<<<<..<<<..<<<<<.....>>>>>..>>>...<<....>
>.......<<<<<..<<....>>...>>>>>.<<<<<<<<...<<....>
>...>>>>.>>.>>....>>>>.>>>>>>>>>.<<.<...<<<<<<....
.<<<<<<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<
<<.<<.<<........>>>>>>>>....>>>>>>>>>...<<.......>
>......>>>>>>......>.>>...<<<<<......<<<....>>>..<
<<<<<<<<.....<<.<<<<<<<.....<<<........>>.>.....>>
>>>...<<<<.<<<<.<......>>>>>.>>>>.....>>>>...>>>>>
>>.>>..<<<<.<<<<<.....>>>>>.>>>>....<<<......>>>..
.<<<<<<<...<<<(((.....<<<<<<......<..........<<<.<
<<<<<<<<<.......<<<<<.<<<...<<.........>>...>>>...
......<<......>>...>>>>>...>>>>>>>>>>>>>..........
))).>....>>>>>>.>>>...>>>>>>><<<<<<<<<.........>>>
>>>>>>....>>>>>.<<<<<<<<<<.<<......<<<<.<<<<....>>
>>>>>>...>>>>>>>>>>.>>.....>>>>>><<.....<<.....<<<
<<<.......>>>>>><<<<.....<<<<<.<<...<<<<<<...<<...
..>>.>>>>>>....((<<<<<<...<<<<..<<<....>>>........
<<<<<......>>>>>...>>>>....>>...<<<<<........>>>>>
))<<<<.<<<<.<<<....<<<....>>>...<.{.<<<<<<...<<<<.
<<<<<<<.<<<<<.<<<<...[[..>>>>.><...<<<<<....<<<<<<
....<<<.....>>>....>>>>>>.....>>>>>....><<<<<<<...
...>>>>>>>>>>>...>>>>>>>.>>>>.........>>>>>>...>..
...>>>...>>>>>>>>>>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>>..<<<<.....<<<<<<<.<<..............
.<<<<<....<....>.....>>>>><<.<<<<<<<<<<<.<<<<<..>>
>>>......>>>>>..>>>>>>.>>............<<<<<<<<<..<<
<.........>>>..<<<<<<<....<<<<.....>>>>......>>>>>
>>...........<<..>>......>>.>>>>>>>.....>>.>>>>>>>
..>>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<
........<<<<<.<<<<<<..<<<<<.<<<<<<<<..<<<<<<..>>>>
>>...<<<<<.....<<<<..<<<<<....>>>>>...........}..<
<<<<.....>>>>>..>>>>..>>>>>.....>>>>>>>>..>>>>>...
....<<<<<<.<<<<<<....>>>>>>>>...<<<<<<<...<<<<<<..
.....>>>>>>.....<<......>>....>>>>>>>....<<<<.<.<<
<.....>>>.>>>>>.<<<....>>>..>>>>.<<...<<<<<<<..<<<
<.))))))>>>>>>>>>>>.....>>..>>>>..>>>>>>>.........
<<<<<<...<<.......>>...>>>>>>...............<<<<..
.<<<<..<.<<<<<<<......>>>>>>>...>.<<<.........>>>.
....>>>>.......>>>>......<<<<<<<....>>>.>>>>......
..>>>.>>>>>....<<<<<<<..<<<<.<.<<<<<..............
...>>>>>.><<<<<...<<<<....<<<<<<<<<<]]..>>>>>..>>>
>>...>>>>..>>>>>.<<<<...<<<<<...........>>>>>...>>
>>.>>>>....>>>>>>>.....<<<<<.<<.<<<......<<.......
<<<<..>>>>....>>........<<<<.....<<<.<<<<<.......>
>>>>.>>>....>>>>..............>>>>>.>>>>>...<<<<<<
<.............>>....<<<<<<<<<.<<<....<<<<....<<<<<
......>>>>>...>>>>...>>>....>>>>..>>>>>...>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pv3 Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		M1 K2 V3 R4 P5 V7 S8 S9 R11 K13 A14 R15 H18 V28 S31 P33 K36 R45 S46 V58 R59 G60 A61 K76 R86 K88 A89 T90 H99 S101 N102 R120 G124 R125 Q127 V128 K132
Binding residue
(residue number reindexed from 1)		M1 K2 V3 R4 P5 V7 S8 S9 R11 K13 A14 R15 H18 V28 S31 P33 K36 R45 S46 V58 R59 G60 A61 K76 R86 K88 A89 T90 H99 S101 N102 R120 G124 R125 Q127 V128 K132
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0002181 cytoplasmic translation
GO:0006412 translation
GO:0042273 ribosomal large subunit biogenesis
Cellular Component
GO:0005840 ribosome
GO:0015934 large ribosomal subunit
GO:0022625 cytosolic large ribosomal subunit

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8pv3, PDBe:8pv3, PDBj:8pv3
PDBsum8pv3
PubMed37921038
UniProtG0RYN9

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