Structure of PDB 8rjd Chain Y Binding Site BS01

Receptor Information

>8rjd Chain Y (length=134) Species: 9984 (Oryctolagus)

MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIR
KDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIH
PSKVVITRLKLDKDRKKILERKAKSRQVGKEKGK

Ligand information

>8rjd Chain K (length=3543)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccggggggcccaaguccuucu
gaucgaggcccagcccguggacggugugaggccgguagcggcccccggcg
cgccgggcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcgcgguccggccgugccggcggggcgg
aucucccgcucccgucggcgggggaccgccccccggccggcgaccggccg
ccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggac
ggcugggaaggccccggcggggaagguggcccgggggccccggguguuac
agccccgccccggcagcagcagcucgccgaaucccggggccgagggagcg
agacccgugcgccgcgcucuccccccucgggggggccgggccaccccucc
cacggcgcgaccgcuggggcggacuguccagugcgccccgggcgggucgc
gccgucgggcccggggggccacgcgucccccgcgagcgcacggggucggc
ggcgaugucggcuacccacccgacccgucuugaaacacggaccaaggagu
cuaacacgugcgcgagucgggggcuacgaaagccgccguggcgcaaugaa
ggugaaggccggcggcgcgccgccggccgaggugggaucccgaggccuuc
caguccgccgagggcgcaccaccggcccgucucgcccgccgcgccgggga
gguggagcacgagcgcacguguuaggacccgaaagauggugaacuaugcc
ugggcagggcgaagccagaggaaacucugguggagguccguagcgguccu
gacgugcgaaucggucguccgaccuggguauaggggcgaaagacuaaucg
aaccaucuaguagcugguucccuccaaaguuucccucaggauagcuggcg
cucuccgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccg
aaacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcuc
gcugguguggagccgggcguggaaugcgagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
gcaggaugguggccauggaagucggaauccgcuaaggaguguguaacaac
ucaccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgg
gcccauacccggccgucgcuggcagucggcagagcgagaaagagaguggc
gcggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaa
gccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggugg
uaguagcaaauauucaaacgagaacuuugaaggccgaaguggagaagggu
uccaugugaacagcaguugaacaugggucagucgguccugagagaugggc
gagcgccguuccgaagggacgggcgauggccuccguugcccucagccgau
cgaaagggagucggguucagauccccgaauccggaguggcggagaugggc
gccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcg
ggagccccggggagaguucucuuuucuuugugaagggcagggcgcccugg
aauggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguu
ccggcggcguccggugagcucucgcuggcccuugaaaauccgggggagag
gguguaaaucucgcgccgggccguacccauauccgcagcaggucuccaag
gugaacagccucuggcauguuggaacaauguagguaagggaagucggcaa
gccggauccguaacuucgggauaaggauuggcucuaagggcuggcagccg
acuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaa
gcaucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccag
ugcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcg
ggaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauua
gugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuau
ccagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaa
gaagacccuguugagcuugacucuagucuggcacggugaagagacguuuu
uucacugacccggugaggcgggggggcgagccgggcucucgcuucuggcg
ccaagcgcccggccggccgggcgcgacccgcuccggggacagugccaggu
ggggaguuugacuggggcgguacaccugucaaacgguaacgcaggugucc
uaaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaa
agcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcgggg
ccucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaa
guuaccacagggauaacuggcuuguggcggccaagcguucauagcgacgu
cgcuuuuugauccuucgaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcuggguu
uagaccgucgugagacagguuaguuuuacccuacugaugauguguuguug
ccaugguaauccugcucaguacgagaggaaccgcagguucagacauuugg
uguaugugcuuggcugaggagccaauggggcgaagcuaccaucuguggga
uuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauagc
gccggagccucgguuggccucggauagccggucccccgccgggguccggu
gcggagagcccuucgucccgggaaacggggcggccggaaagggggccgcc
cucucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaacca
uucguagacgaccugcuucugggucgggguuucguacguagcagagcagc
ugcugcgaucuauugaaagucagcccucgacacaaggguuugu

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....>>>>.....((......<<<.....))>>>...>.>>>>>>>...>
>>>>>>>...>>>>>>>>>.......<<<<<<<........>>>>>>>..
...<<<<<..((((((>>>>>..>>>........................
..........<<....>>...............<<<......>>>.....
.............................<<<<<<<<..<<<.<....<<
<<<<<<.<<<.....<<<<<<<<<<....<<<<<<<.<<<<<.<<<<<<<
.<<<<<<<<<......>>>>>>>>>>>>>>>>>>>>>>>>>...>>>.>>
>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<<<
<<<...<<..<<<..<<<<<<<......<<<<<<<<.>>>>>>>>.....
..>>>>>>>..>>>.........>>>>>>..>>>>>>>>>>>.....<<.
....{.>>.........<...<<<<<<..>>>>>>...<.<<..<<<.<<
<<<<<<<<<<<<<<<<<<<<<.<<<<..>>>>.>>>>>>.>>>.>>>>>>
>>>>>.>>>...>>>>>.>................>........>>>.>>
>>>....>>>>...>>>>>>>>..<<<<........>>>><<<<<<....
<<<<<<<<<<<<<..<<<...<<<<.....>>>>.....>>>...<<...
.>>...<<<<<<<<<<..>>>>>>>>>>..<<<<<...<<<..<<<...(
((.[[.>>>..>>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>
>>>>>.>>....>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<
<<<<..<<<....<<<<<<<....>>>>>>>.....>>>...<<<..<<.
<<........>>>>.>>>....>>>>>>>>>...<<.......>>.....
.>>>>>>...>..>.>>..<<<<<<....<.<<<....>>>.><<.<<<<
<<<...<<<.<<<<<<<<<...<<<....<<<..<.<<<..<<<<<<.<.
....>.>>>>>>>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<
.<......>>>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<
.....>>>>>.>>>>....<<<......>>>...<<<<<<<...<<<(((
.......<<<<<.....<<..........<<<.<<<<<<<<<<.......
<<<<...<<....<..........>...>>....................
...>.>>>...>>>>>>>>>>>>>..........))).>>...>>>>>..
>>>...>>>>>>><<<<<<.<<<........}...........]].))).
...........>>>>>>>>>....>>>>>>...<<<<<<<<.<<......
<<<<.<<<<....>>>>>>>>...>>>>>>>>>>........>>>>>><<
.....<<.....<<<<<<.......>>>>>>.<<<<....<<<<<.<<..
.<<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<
....>>>..........<<.<<<<<<<<<...>>>>>>>>>>>......>
>....>>>..<<<<<........>>>>>))<<<<....<<<<<...<<<<
<<<....>>>>>>>...<<<....>>>...<..<<<<<<<...<<<<<<<
<<<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<<<<..
...<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<....
...>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>>..>..
........>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<
<<.....>>>>.>>>>....<<<<.....<<<<<<<.<<...........
....<<<<<.....<..>......>>>>><<.<<<<<<<<<<<.>>>>>.
.>>>>>>.>>............<<<<<<<<<..<<<.........>>>..
<<<<<<<....<<<<.....>>>>......>>>>>>>...<<..<<<..<
<<<<<....<<<.....<<<<....>>>>.....>>>.>>>>..>>>>><
<<<<<.......>>>>>>........<...........<<<<<.......
>>>>>.....>.....>>....>>.>>>>>>>.....>>.>>>>>>>..>
>>>>>....>>....<<<<<........>>>>>....<<<<<..<<<.<<
......<<<<.<<<<<<..<<<<<.<<<<<<<<<.<<<<<<<<<..>>>>
>>>>>...<<<<<.....<<<<..<<.<..<<>>..>.>>..........
....<<<<<<<<<..>>>>>>>>>..>>>>..>>>>>....>>>>>>>>>
..>>>>>...<<<.....>>>..<<<<<<...........>>>>>>..<<
...<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>...
.>>>>>>>...<<<..<<<<.......>>>>..>>><<<<....>>>>>>
)))].....<<<<<<<..<<<..)))))).>>>>>>>>>>.........>
>>>..>>>>>>.......<<.<.<.<<<<<<...<<.......>>...>>
>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.<<<<<......>
>>>>...>.>.<<<.........>>>.....>>>>>..>...>>>.>>..
..<<<<<<<....>>>.>>>>....>>..>>>.>>>>>.....<<<<<<.
<..<<<..<.<<<<<.................>>>>>.><<<<....<<<
<....<<.<<<<<<<]]].>>>>>..>>.>>...>>>>...>>>><<<<<
...<<<<<...........>>>>>...>>>>>.>>>...>.>>>>>>.<<
<<<<<..<<<<....<<<........<<<<<..<<<<<.>>>>>.>>>>>
.......>>>...<<<..<<<<....<<<<<<<<..........>>>>>.
>>>...>>>>..>>>..............>>>>..>.>>>>>>.<<<<<.
<.............>....<<.<<<<<<<.<<.....<<<<.<..<<<<<
.>>>>>..>>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rjd UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
• Resolution: 2.78574 Å
• Binding residue (original residue number in PDB): M1 K2 F3 N4 P5 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 K36 R39 R45 S46 V58 R59 G60 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126
• Binding residue (residue number reindexed from 1): M1 K2 F3 N4 P5 T8 S9 R11 K13 N14 R15 R17 H18 K28 S31 P33 K36 R39 R45 S46 V58 R59 G60 H61 K63 R87 K89 A90 N91 H100 S102 K103 R121 K122 S125 R126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0048027 mRNA 5'-UTR binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006364 rRNA processing
• GO:0006412 translation
• GO:0006977 DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
• GO:0034644 cellular response to UV
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0071479 cellular response to ionizing radiation
• GO:0071480 cellular response to gamma radiation
• GO:1902164 positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator
• GO:1902167 positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
• GO:1904803 regulation of translation involved in cellular response to UV

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8rjd, PDBe:8rjd, PDBj:8rjd
• PDBsum: 8rjd
• PubMed: 38896445
• UniProt: G1SQH0|RL26_RABIT Large ribosomal subunit protein uL24 (Gene Name=RPL26)