Structure of PDB 8b5l Chain g Binding Site BS01

Receptor Information

>8b5l Chain g (length=114) Species: 9986 (Oryctolagus cuniculus)

VQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKKVGKAPKSACGVCPG
RLRGVRAVRPKVLMRLSKTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQK
IVVKVLKAQAQSQK

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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<<<<<<<.<<<<...<<..<<<.<<<<<<<......<<<<<<<<<<....
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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): V2 R4 L5 T6 Y7 R8 R9 R10 S12 Y13 T15 R21 L22 R24 T25 P26 G27 N28 Y32 Y34 K36 K37 K40 P42 K43 V48 R54 G55 R60 P61 K62 L64 R66 K69 T70 K72 H73 V74 S75 R76 Y78 G79 G80 R90 R93 I97 E98 Q100
• Binding residue (residue number reindexed from 1): V1 R3 L4 T5 Y6 R7 R8 R9 S11 Y12 T14 R20 L21 R23 T24 P25 G26 N27 Y31 Y33 K35 K36 K39 P41 K42 V47 R53 G54 R59 P60 K61 L63 R65 K68 T69 K71 H72 V73 S74 R75 Y77 G78 G79 R89 R92 I96 E97 Q99

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• 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: G1TXG5|RL34_RABIT Large ribosomal subunit protein eL34 (Gene Name=RPL34)