Structure of PDB 8b5l Chain J Binding Site BS01

Receptor Information

>8b5l Chain J (length=170) Species: 9986 (Oryctolagus cuniculus)

KENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTV
RSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGF
GIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRI
SKEEAMRWFQQKYDGIILPG

Ligand information

>8b5l Chain 5 (length=3619)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggaaau
guggcguacggaagacccacuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggccggccgugccggcgguc
ucggcggaucuuucccgcucccgggggcgggggaccgccccccggccggc
gaccggccgccgccgggcgcauuuccaccgcggcggugcgccgcgaccgg
cuccgggacggcugggaaggcccggcggggaagguggcccggggggacgc
cucgccggcgggcgcgaccccuccccggguguuacagccccgccccggca
gcagcagcucgccgaaucccggggccgagggagcgagaccugugucgccg
cgcucuccccccugggggggccgggccaccccucccacggcgcgaccgcu
ggggcggacuguccccagugcgccccgggcgggucgcgccgucgggcccg
ggggccacggcgcgucgcggcgcgcgcgagcgagcgcacggggucggcgg
cgaugucggcuacccacccgacccgucuugaaacacggaccaaggagucu
aacacgugcgcgagucgggggcucgcacgaaagccgccguggcgcaauga
aggugaaggccggcgucgccggccgaggugggaucccgaggccuuccagu
ccgccgagggcgcaccaccggcccgucucgcccgccgcgccggggaggug
gagcacgagcgcacguguuaggacccgaaagauggugaacuaugccuggg
cagggcgaagccagaggaaacucugguggagguccguagcgguccugacg
ugcgaaucggucguccgaccuggguauaggggcgaaagacuaaucgaacc
aucuaguagcugguucccuccaaaguuucccucaggauagcuggcgcucu
cgcccgcaguuuuauccgguaaagcgaaugauuagaggucuuggggccga
aacgaucucaaccuauucucaaacuuuaaauggguaagaagcccggcucg
cugguguggagccgggcguggaaugcgagugccuagugggccacuuuugg
uaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgccc
gaugccgacgcucaucagaccccagaaaagguguugguugauauagacag
caggaugguggccauggaagucggaauccgcuaaggaguguguaacaacu
caccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucggg
cccauacccggccgucgcuggcagucggcagagcgagaaagagaguggcg
cggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaag
ccuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggu
aguagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguu
ccaugugaacagcaguugaacaugggucagucgguccugagagaugggcg
agcgccguuccgaagggacgggcgauggccuccguugcccucagccgauc
gaaagggagucggguucagauccccgaauccggaguggcggagaugggcg
ccgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcgg
gagccccggggagaguucucuuuucuuugugaagggcagggcgcccugga
auggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuc
cggcggcguccggugagcucucgcuggcccuugaaaauccgggggagagg
guguaaaucucgcgccgggccguacccauauccgcagcaggucuccaagg
ugaacagccucuggcauguuggaacaauguagguaagggaagucggcaag
ccggauccguaacuucgggauaaggauuggcucuaagggcuggcagccga
cuuagaacuggugcggaccaggggaauccgacuguuuaauuaaaacaaag
caucgcgaaggcccgcggcggguguugacgcgaugugauuucugcccagu
gcucugaaugucaaagugaagaaauucaaugaagcgcggguaaacggcgg
gaguaacuaugacucucuuaagguagccaaaugccucgucaucuaauuag
ugacgcgcaugaauggaugaacgagauucccacugucccuaccuacuauc
cagcgaaaccacagccaagggaacgggcuuggcggaaucagcggggaaag
aagacccuguugagcuugacucuagucuggcacggugaagagacaugaga
acuccgaucguuuuuucacugacccggugaggcgggggggcgagccgggc
ucucgcuucuggcgccaagcgcccggccccggggccgggcgcgacccgcu
ccggggacagugccagguggggaguuugacuggggcgguacaccugucaa
acgguaacgcagguguccuaaggcgagcucagggaggacagaaaccuccc
guggagcagaagggcaaaagcucgcuugaucuugauuuucaguacgaaua
cagaccgugaaagcggggccucacgauccuucugaccuuuuggguuuuaa
gcaggaggugucagaaaaguuaccacagggauaacuggcuuguggcggcc
aagcguucauagcgacgucgcuuuuugauccuucgaugucggcucuuccu
aucauugugaagcagaauucaccaagcguuggauuguucacccacuaaua
gggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccu
acugaugauguguuguugccaugguaauccugcucaguacgagaggaacc
gcagguucagacauuugguguaugugcuuggcugaggagccaauggggcg
aagcuaccaucugugggauuaugacugaacgccucuaagucagaaucccg
cccaggcggaacgauacggcagcgccgaggagccucgguuggccucggau
agccggucccccgcgggguccggugcggagagcccuucgucccgggaaac
ggggcgcggccggaaagggggccgcccucucgcccgucacgcaccgcacg
uucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggu
cgggguuucguacguagcagagcagcugcugcgaucuauugaaagucagc
ccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8b5l Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative.
• Resolution: 2.86 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 S51 A53 R54 F60 N97 N98 T102 N104 G106 F107 G108 G127 D129 Y131 V133
• Binding residue (residue number reindexed from 1): K12 C14 N16 C18 S44 A46 R47 F53 N90 N91 T95 N97 G99 F100 G101 G120 D122 Y124 V126

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0019843 rRNA binding

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8b5l, PDBe:8b5l, PDBj:8b5l
• PDBsum: 8b5l
• PubMed: 36867692
• UniProt: G1TUB8|RL11_RABIT Large ribosomal subunit protein uL5 (Gene Name=RPL11)