Structure of PDB 8p5d Chain LU0 Binding Site BS01

Receptor Information

>8p5d Chain LU0 (length=100) Species: 1358809 (Spraguea lophii 42_110)

DQSITYTLDCTKCTEQSLFSTDDLKEYLLGNIKYNGKKGQLGKKVLLSNT
GHAVDVFFAKKTSKRYLKYLIKKFLRAKGLSDWVRPIAGDKQSYKFSFFS

Ligand information

>8p5d Chain L50 (length=2499)

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

Structure summary

• PDB: 8p5d Spraguea lophii ribosome
• Resolution: 10.8 Å
• Binding residue (original residue number in PDB): K40 Y41 N42 K50 K51 K71 Y73 K75 Y76 K80 R83 R92 I94
• Binding residue (residue number reindexed from 1): K33 Y34 N35 K43 K44 K64 Y66 K68 Y69 K73 R76 R85 I87

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8p5d, PDBe:8p5d, PDBj:8p5d
• PDBsum: 8p5d
• PubMed: 37709902
• UniProt: S7W958