Structure of PDB 8b5l Chain a Binding Site BS01

Receptor Information

>8b5l Chain a (length=147) Species: 9986 (Oryctolagus cuniculus)

PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPG
YFGKVGMRHYHLKRNQSFCPTVNLDKLWTLVSEQTRVNAAKNKTGAAPII
DVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGVGGACVLVA

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

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): P2 S3 R4 R6 K7 T8 R9 K10 R12 G13 H14 S16 H17 G18 H19 G20 R21 I22 G23 H25 R26 K27 H28 P29 G31 R32 G33 N34 G36 H39 H40 H41 R42 I43 N44 K47 Y52 G54 K55 V56 G57 M58 R59 H60 Y61 H62 L63 K64 R65 Q67 N74 K77 V82 S83 Q85 D102 R105 K110 L112 G113 K114 K116 K119 S130 R131 R132
• Binding residue (residue number reindexed from 1): P1 S2 R3 R5 K6 T7 R8 K9 R11 G12 H13 S15 H16 G17 H18 G19 R20 I21 G22 H24 R25 K26 H27 P28 G30 R31 G32 N33 G35 H38 H39 H40 R41 I42 N43 K46 Y51 G53 K54 V55 G56 M57 R58 H59 Y60 H61 L62 K63 R64 Q66 N73 K76 V81 S82 Q84 D101 R104 K109 L111 G112 K113 K115 K118 S129 R130 R131

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0022625 cytosolic large ribosomal subunit
• GO:0043232 intracellular non-membrane-bounded organelle
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8b5l, PDBe:8b5l, PDBj:8b5l
• PDBsum: 8b5l
• PubMed: 36867692
• UniProt: G1SNY0|RL27A_RABIT Large ribosomal subunit protein uL15 (Gene Name=RPL27A)