Structure of PDB 8agx Chain M Binding Site BS01

Receptor Information

>8agx Chain M (length=135) Species: 4932 (Saccharomyces cerevisiae)

AKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPL
KVTKKHGAKKVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETF
EQPSQREEAKKVVKKAFEERHQAGKNQWFFSKLRF

Ligand information

>8agx Chain f (length=3216)

uugaccucaaaucagguaggaguacccgcugaacuuaagcauaucaauaa
gcggaggaaaagaaaccaaccgggauugccuuaguaacggcgagugaagc
ggcaaaagcucaaauuugaaaucugguaccuucggugcccgaguuguaau
uuggagagggcaacuuuggggccguuccuugucuauguuccuuggaacag
gacgucauagagggugagaaucccguguggcgaggagugcgguucuuugu
aaagugccuucgaagagucgaguuguuugggaaugcagcucuaagugggu
gguaaauuccaucuaaagcuaaauauuggcgagagaccgauagcgaacaa
guacagugauggaaagaugaaaagaacuuugaaaagagagugaaaaagua
cgugaaauuguugaaagggaagggcauuugaucagacaugguguuuugua
uuucacuggccagcaucaguuuugguggcaggauaaauccauaggaaugu
agcuugccucgguaaguauuauagccugugggaauacugccagcugggac
ugaggacugcgacguaagucaaggaugcuggcauaaugguuauaugccgc
ccgucuugaaacacggaccaaggagucuaacgucuaugcgaguguuuggg
uguaaaacccauacgcguaaugaaagugaacguagguuggggccucgcaa
gaggugcacaaucgaccgauccugaugucuucggauggauuugaguaaga
gcauagcuguugggacccgaaagauggugaacuaugccugaauaggguga
agccagaggaaacucugguggaggcucguagcgguucugacgugcaaauc
gaucgucgaauuuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguuccugccgaaguuucccucaggauagcagaagcucguaucaguu
uuaugagguaaagcgaaugauuagagguuccggggucgaaaugaccuuga
ccuauucucaaacuuuaaauauguaagaaguccuuguuacuuaauugaac
guggacauuugaaugaagagcuuuuagugggccauuuuugguaagcagaa
cuggcgaugcgggaugaaccgaacguagaguuaaggugccggaauacacg
cucaucagacaccacaaaagguguuaguucaucuagacagccggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccggccga
augaacuagcccugaaaauggauggcgcucaagcguguuaccuauacucu
accgucaggguugauaugaugcccugacgaguaggcaggcguggagguca
gugacgaagccuagaccguaaggucgggucgaacggccucuagugcagau
cuuggugguaguagcaaauauucaaaugagaacuuugaagacugaagugg
ggaaagguuccacgucaacagcaguuggacguggguuagucgauccuaag
agauggggaagcuccguuucaaaggccugauuuuaugcaggccaccaucg
aaagggaauccgguuaagauuccggaaccuggauauggauucuucacggu
aacguaacugaauguggagacgucggcgcgagcccugggaggaguuaucu
uuucuucuuaacagcuuaucaccccggaauugguuuauccggagaugggg
ucuuauggcuggaagaggccagcaccuuugcuggcuccggugcgcuugug
acggcccgugaaaauccacaggaaggaauaguuuucaugccaggucguac
ugauaaccgcagcaggucuccaaggugaacagccucuaguugauagaaua
auguagauaagggaagucggcaaaauagauccguaacuucgggauaagga
uuggcucuaagggucggguacgaucaacuuagaacugguacggacaaggg
gaaucugacugucuaauuaaaacauagcauugcgauggucagaaagugau
guugacgcaaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaccaagcgcggguaaacggcgggaguacucucuuaagguagccaa
augccucgucaucuaauuagugacgcgcaugaauggauuaacgagauucc
cacugucccuaucuacuaucuagcgaaaccacagccaagggaacgggcuu
ggcagaaucagcggggaaagaagacccuguugagcuugacucuaguuuga
cauugugaagagacauagaggguguagaauaagugggagcuucggcgcca
gugaaauaccacuaccuuuauaguuucuuuacuuauucaaugaagcggag
cuggaauucauuuuccacguucuagcauucaaggucccauucggggcuga
uccggguugaagacauugucagguggggaguuuggcuggggcggcacauc
uguuaaacgauaacgcagauguccuaaggggggcucauggagaacagaaa
ucuccaguagaacaaaaggguaaaagcccccuugauuuugauuuucagug
ugaauacaaaccaugaaaguguggccuaucgauccuuuagucccucggaa
uuugaggcuagaggugccagaaaaguuaccacagggauaacuggcuugug
gcagucaagcguucauagcgacauugcuuuuugauucuucgaugucggcu
cuuccuaucauaccgaagcagaauucgguaagcguuggauuguucaccca
cuaauagggaacgugagcuggguuuagaccgucgugagacagguuaguuu
uacccuacugaugaauguuaccgcaauaguaauugaacuuaguacgagag
gaacaguucauucggauaauugguuuuugcggcugucugaucaggcauug
ccgcgaagcuaccauccgcuggauuauggcugaacgccucuaagucagaa
uccaugcuagaacgcggugauuucuuugcuccacacaauauagauggaua
cgaauaaggcguccuuguggcgucgcugaaccauagcaggcuagcaacgg
ugcacuuggcggaaaggccuugggugcuugcuggcgaauugcaaugucau
uuugcguggggauaaaucauuuguauacgacuuagauguacaacggggua
uuguaagcaguagaguagccuuguuguuacgaucugcugagauuaagccu
uuguugucugauuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8agx Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): G16 R17 H36 F38 R48 T54 K55 G58 K64 R65 K67 K69 K73 V74 N76 N78 H79 R107 E108 K111 K112 K115 K133 R135 F136
• Binding residue (residue number reindexed from 1): G15 R16 H35 F37 R47 T53 K54 G57 K63 R64 K66 K68 K72 V73 N75 N77 H78 R106 E107 K110 K111 K114 K132 R134 F135

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0022625 cytosolic large ribosomal subunit
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8agx, PDBe:8agx, PDBj:8agx
• PDBsum: 8agx
• PubMed: 36804914
• UniProt: P0C2H6|RL27A_YEAST Large ribosomal subunit protein eL27A (Gene Name=RPL27A)