Structure of PDB 8p5d Chain LJ0 Binding Site BS01

Receptor Information
>8p5d Chain LJ0 (length=167) Species: 1358809 (Spraguea lophii 42_110) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENPMNKIKIQKLCLNICTGGGEILNKASKVLEQLTGQKPRLSKSRLTIRS
FGIRRNEKIACHVTVRGEKAMEILEKGIKIKEYELIDSNFSTQGSFGFGI
KEHIDMGIKYEPDVGIFGMNFYVVLEKPGIRVSKRKRVKSRVGNKQRVTK
DEAKNWFVKKYEGIVLG
Ligand information
>8p5d Chain L50 (length=2499) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auaccacacacaagggaucguuuggcuccugggacgaggaagggcgcagc
agagagcgauaugugugggagcagcagcaaugaccacacguccccgaaua
cagcauagugcuggaguacuccuuggaauuaagcauaugaguaaaggaag
gaaaagaaacuaacgaggauucccguaguagcggcgagugaacagggaac
aguccaacaguguaauucucaaaugagaaguugucaaaaggaagaagaug
ugaaucagaaagaaaagcugaacgauacagggugauagucccguaguguc
uucuuacauacggugaguagcugugcucgguaaugcacagugaagaggug
gcagugugcaucuaagacuaaauacaacaggagaccgauagcaaagaagu
agguugaccgaaaacagugaaauuguguguggacccgaauggaucgggcc
cgucuugaaacacggaccaaggagugcacauacacugcaaguugagcaga
ggaagucugugaggcguagugaagacggaaagcagugugagugcgacccg
auagacuugugaacuauaccuuguugcugugaaggcuggcgaaagccagc
uggaggcggcaagccguauugaucugcaaaucauuggcguaagcagggua
uaggggcgaaagaccaaucgaacagucuaguugcugguucccuccgaaau
gucuaucaggacagcgcgcacgcagagagaagcaagguagagcaugggcc
gguauccuuaaggagacggacgaacugcgaaugugcuuuucuucuaugca
agcguagugggcgaguucugguaagcaggacuggcgaagaggaaugaacc
uggcacugugcuaaggaacccaaugucuggacagagaccgaaagagguag
gugaauaaaauucaucugcucugaaaauugauggcgcuuaccagacaucc
gaugcacaguuagcagguaggagggcgugugucuacuggcgaagguaccg
agugaucggugguggagguagaugcagagcagaucuuggugguaguagcg
auaauuugucuucagcggcaaagacugaggaggagaaggguuucuucuca
uaagaagagugagccgggucuaagcgaguguguagaagcaugagcgaagg
agaaacagguugauauuccugugccugugcugucguacggcaacguguau
uagcuugucgacacgaacaucuagacaaagcagaaacaccuuuucuguuc
aaggggaaaaagaccacugagacggaucaucuggcgacgugguuuuauau
cugugaccaggccugagccugguuuguugaggauggucguccaugaaaag
acaacuauauggcagcacaguccguaccaaccguaucaggacuccaaggu
gaagagccucuaguggauguuuuacacauguaagggaauucggcaaaaug
gaugcguaacuucgggagaaguauugguucaauugugaacucauugugac
aaggggaaucugacuguuuaguaaaaacauagcuucaugaagagagauga
agugaguucugcccggugcucggucgugacacggaggaaaugccagaaag
cacggguuaacggcgggaguaacuaugacucucuuaagguagccaaacgc
cucgucauuuaaauggugacgcgcaugaauggaaugacgagauucccacu
gucccuacauguagacuagcgaacccauuuccaggggaacgggccuggac
ggccagcggggaaagaagacccuguugagcuugacucuaguguggccaag
uugugacgauugaggcgagcgccaugaucaucacgacacacuuguuuaag
gacaaaggccagauggggaguuuggcuggggcgguacgaccacagaauca
gaacguggucgaccgaagguacucacagcgagacgagaacacucguguag
agcauaaggacuaaagagugccugagugugagcacuacugcuugcaugag
gggaaacccgggccuagcgauccuacgcauacgagacacuuguggcgugg
gugucagaaaaguuaccacagggauaacuggcuuguggccgccgagcgua
gaaagcgacgcggcuuuuugauucuucgaugucggcucuuccuagcaugg
ccaugcagccguggcgaaguguuggauuguucacccacuaacagggaacg
ugagcuggguuuagaccgucgugagacagguuaguuuuauccuacugucc
aaacaguugaagggaguguggauuaguacgaaaggaaacccacacgugac
cucuggugcagcgggugugcggaagugcaacugccaugcuacgucuccuc
aagcauagcuggaagccucuaagcuagaaaugaguccugacucuggaaga
cggccgggaagacgacccguaguuaacagcgguguuguacgauaugagcu
uucuauuguaguagcgaguauuugagacacugguuguuaccaccgucgu
....<<<<<<<<<......((..((<<<<<<...<......<<<<<<.((
.....>>>....<<<<<<..<..))..>.....>>>>>>...>>>.....
<<<<<...>>>>>>....<<<<<<.....<......>......>>>>>.>
.........<<....>>..<<<<<......<<.....>>.....>>>>>.
.<<<...........<<<<<<..>>>>>>............<<<<<<<<<
<...<<<<.........>>>>((......<<<.....))>>>...>>>>>
>>>>>..............<<<<<<<........>>>>>>>....<<<<<
..<<<<<.>>>>>..>>>.........>>>>>>.))..............
.<<....>>....)).......>>>>>>>>>..<<<<<.....>>>>>.<
<<<........>>>><<<<<<....<<<<.<<<<<<<<..<<<..<<<<<
.....>>>>>..>>>...<<....>>.....>>>>>>>>.>>>>..<<.<
..<<<<<.<<.....<<<<<<<<<<<<<<....<<<<<<<....>>>>>>
>.....>>>>>.<<<..<<.<<........>>>>.>>>....>>>>>>>>
>...<<.......>>......>>>>>>...>..>.>>..<<<<<<....<
<<<<....>>>>><<<<<<..<<<<<.<<<<<<<.....<<<......<<
<...<<<<..>>>>..>>>.....>>.>.....>>>>>..>>>>>..>>.
.>>>>.>>..<<.<<<<<<<.....>>>>>>>.>>....<<<......>>
>...<<<<<<<...<<<.((...<<<<<<<.....<......<<.<<<<<
<<<<<<...>>>>>>>>>>>>>..........))..>...>>>>>>>>>>
...>>>>>>>.........>>>>>><.<<<<<<<<<<......<.<<<<<
<....>>>>>>.>...>>>>>>>>>>..>.....>>>>>><<.....<<.
....<<<<<<......>>>>>>.<<<.....<<<<..<<...<<<<<<..
..>>>>>>....((<<<<<<...<<..<<<<......>>>>..>>....>
>...<<<<<........>>>>>))<<<<<<<<<<..<<<....>>>....
<<<.<<<<<...<<<<.<<<<..<<<<<<<<<<<<...[[..>>>>>><<
..<<<..<.<<<<<<<<.....<<<<...>>>>.....>>>>>>>>.>.>
>>..>><<<<<<....>>>>>>>>>>>>...>>>>.>>>>.........>
>>>>>>>...>>>>>>>>>>>>>>..>>..<<......>>.>>>>.<<<<
.....>>>>..>>>....<<.....<<<<<<<.<<.........<.....
<<<<<.....<..>......>>>>><<<<<<....>>>>>>.........
...<<<<<<<<<..<<<.........>>>..<<<<<<<........>>>>
>>>..<<<..<<<..<<<<<<<.<.<<.....<<........>>.....>
>>>>>>>..>>>>><<<<<<.......>>>>>>........<........
...<<<<<<.....>>>>>>.....>.....>>.>..>>.>>>>>>>..>
..>>.>>>>>>>..>>..>>....>>....<<<<<........>>>>>..
[[.<<<..<<<.[[......<<<<.[[<<<<..<<<<<.<<.<<<<<..<
<<<<<<.<<<<..<<<<..>>>>..>>>>.>>>>>>>...<<<....>>>
......>>>>>.>>..>>>>>...<.<.....>.>..<<<<<<.......
....>>>>>>..<<...<<<<<<<...<<<<<.........>>>>>....
<<..[.(((.>>...>>>>>>>...<<<<<<<<......>>>>>>>>..<
<<....>>>.>>)))]......<<<<<<.<<<...>>>>>.>>>>>>>>>
..........>>>>..]]>>>>.......<<.<.<.<<<<<<...<<...
....>>...>>>>>>...>>..>>.......<<<<<.<<<<<<..<<<.<
<<<<......>>>>>...>>>.<<<.........>>>.....>>>>>..>
...>>>.>>....<<<<<<<....>>>.>>>>....]]..>>>.>>>.]]
...<<<....<<<<.<<<<<<..................>>>>>><.<<<
...<<<<...<<<<.<<<<.]]...>>>>.>>>>...>>>>.>>>.><<<
<....<<<<<...........>>>>>....>>>>>>>>....>>>...<<
<<<.<<<<.......>>>>....<<<<<<<<<<<<<....<<<<<..<<<
..<<<...>>>.>>>..>>>>>...>>>>>>.>>>>>>>...>>>>>..
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8p5d Spraguea lophii ribosome
Resolution10.8 Å
Binding residue
(original residue number in PDB)
C20 S45 R48 F54 I56 I62 H65 T95 G100 G102 G121 N123 Y125 K137 K139 R144
Binding residue
(residue number reindexed from 1)
C17 S42 R45 F51 I53 I59 H62 T92 G97 G99 G118 N120 Y122 K134 K136 R141
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
Biological Process
GO:0006412 translation
Cellular Component
GO:0005840 ribosome
GO:0022625 cytosolic large ribosomal subunit
GO:1990904 ribonucleoprotein complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8p5d, PDBe:8p5d, PDBj:8p5d
PDBsum8p5d
PubMed37709902
UniProtS7WB69

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