Structure of PDB 6xa1 Chain j Binding Site BS01

Receptor Information

>6xa1 Chain j (length=373) Species: 9606 (Homo sapiens)

NVEIWKIKKLIKSLEAARGNGTSMISLIIPPKDQISRVAKMLADEFGTAS
NIGSRVNRLSVLGAITSVQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKV
NIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFGFIVIDGSGALFGT
LQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAV
QLFISGDKVNVAGLVLAGSADFKTELSQSDMFDQRLQSKVLKLVDISYGG
ENGFNQAIELSTEVLSNVKFIQEKKLIGRYFDEISQDTGKYCFGVEDTLK
ALEMGAVEILIVYENLDIMRYLTPPLLEWFANNYKKFGATLEIVTDKSQE
GSQFVKGFGGIGGILRYRVDFQG

Ligand information

>6xa1 Chain L5 (length=3510)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgggggcgcgggacaugugg
cguacggaagacccgcuccccggggggcccaaguccuucugaucgaggcc
ccguggacggugugaggccgguagcggcccccgggcccgggucuucccgg
agucggguugcuugggaaugcagcccaaagcgggugguaaacuccaucua
aggcuaaauaccggcacgagaccgauagucaacaaguaccguaagggaaa
guugaaaagaacuuugaagagagaguucaagagggcgugaaaccguuaag
agguaaacgggugggguccgcgcaguccgcccggaggauucaacccggcg
gcggguccggccgggcggaucugggaccguccccggccgccgccgggcgc
auuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaagg
cccggcggggaagguggcucggccgaguguuacagcccccccggcagcag
cacucgccgaaucccggggccgagggagcgagacccgucgccgcgcucuc
cccccugggggggccgggccaccccucccacggcgcgaccgcuggggcgg
acuguucccagugcgccccgggcgggucgcgccgucgggcccggggggcc
acgcgcgcgucccgggacggcggagcgagcgcacggggucggcggcgacg
ucggcuacccacccgacccgucuugaaacacggaccaaggagucuaacac
gugcgcgagucgggggcucgcacgaaagccgccguggcgcaaugaaggug
aaggccggccgaggugggaucccgaggccucuccaguccgccgagggcgc
accaccggcccgucucgcccgccgcgccggggagguggagcacgagcgca
cguguuaggacccgaaagauggugaacuaugccugggcagggcgaagcca
gaggaaacucugguggagguccguagcgguccugacgugcaaaucggucg
uccgaccuggguauaggggcgaaagacuaaucgaaccaucuaguagcugg
uucccuccgaaguuucccucaggauagcuggcgcucucgcagacccgacg
cccgccacgcaguuuuauccgguaaagcgaaugauuagaggucuugguca
accuauucucaaacuuuaaauggguaagaagcccggcucgcuggcgugga
gccgggcguggaaugcgagugccuagugggccacuuuugguaagcagaac
uggcgcugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacg
cucaucagaccccagaaaagguguugguugauauagacagcaggacggug
gccauggaagucggaauccgcuaaggaguguguaacaacucaccugccga
aucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccg
gccgucgccggcagucgagaguggacgggagcggcgggccggagccccgc
ggacgcuacgccgcgacgaguaggagggccgcugcggugagccuugaagc
cuagggcgcgggcccggguggagccgccgcaggugcagaucuugguggua
guagcaaauauucaaacgagaacuuugaaggccgaaguggagaaggguuc
caugugaacagcaguugaacaugggucagucgguccugagagaugggcga
gcgccguuccgaagggacgggcgauggccuccguugcccucggccgaucg
aaagggagucggguucagauccccgaauccggaguggcggagaugggcgc
cgcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggg
agccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaa
uggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguucc
ggcggcguccggugagcucucgcuggcccuugaaaauccgggggagaggg
uguaaaucucgcgccgggccguacccauauccgcagcaggucuccaaggu
gaacagccucuggcauguuggaacaauguagguaagggaagucggcaagc
cggauccguaacuucgggauaaggauuggcucuaagggcugggucggucg
cggccggcgccuagcagccgacuuagaacuggugcggaccaggggaaucc
gacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcggguguugac
gcgaugugauuucugcccagugcucugaaugucaaagugaagaaauucaa
ugaagcgcggguaaacggcgggaguaacuaugacucucuuaagguagcca
aaugccucgucaucuaauuagugacgcgcaugaauggaugaacgagauuc
ccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggcu
uggcggaaucagcggggaaagaagacccuguugagcuugacucuagucug
gcacggugaagagacuuuuuucacugacccggugaggcgggggggcgagc
ucucgcuucuggcgccaagcgcccggcgccgggcgcgacccgcuccgggg
acagugccagguggggaguuugacuggggcgguacaccugucaaacggua
acgcagguguccuaaggcgagcucagggaggacagaaaccucccguggag
cagaagggcaaaagcucgcuugaucuugauuuucaguacgaauacagacc
gugaaagcggggccucacgauccuucugaccuuuuggguuuuaagcagga
ggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgu
ucauagcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauu
gugaagcagaauucaccaagcguuggauuguucacccacuaauagggaac
gugagcuggguuuagaccgucgugagacagguuaguuuuacccuacugau
gauguguuguugccaugguaauccugcucaguacgagaggaaccgcaggu
ucagacauuugguguaugugcuuggcugaggagccaauggggcgaagcua
ccaucugugggauuaugacugaacgccucuaagucagaaucccgcccagg
cggaacgauacagcgccgcggagccucgguuggccucggauagccggucc
cggguccggugcggagugcccuucguccugggaaacggggcgcggccgga
gaggcggccgcccccucgcccgucacgcaccgcacguucguggggaaccu
ggcgcuaaaccauucguagacgaccugcuucugggucgggguuucguacg
uagcagagcagcucccucgcugcgaucuauugaaagucagcccucgacac
aaggguuugu

.........................<<<<<<.....<......>......
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>>>..<<<<<<<<<<...<<..<<<<<<<<....<<<<......>>>>.(
(......<<<.....))>>>...>.>>>>>>>.>>..>>>>>>>>>>...
....<<<<<<<........>>>>>>>.....<<<<<..((((((>>>>>.
.>>>..................................<<....>>....
...........<<<<....>>>>...........................
.......<<<<<<<<..<<<.<<...<<<<<<<<.<<<.....<<<<<<<
<<<<..<<<....<<<<<.<<<.>>>>>>>>..>>>>>>>>>>>>>>...
...>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<.<<<<...<<..<
<<....<<<<......<<<<<..>>>>>.......>>>>...>>>.....
...>>>>>>...>>>>>>>>>>....................<<<<<<.<
<<<<<..>>>>>>.<<<<<<.<<<<.<<<<<<<<<<<.<<<<<<<<<<<.
<<<<....>>>>.>>>>>>>.>>>>.>.>>>>>>>.>>>...>>>>>>>>
.>>..<<<<<<<..>>>>>.>>....>>>>>>......>>.>>>>>...>
>>>>...>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<
<<<<<<..<<<...<<<<........>>>>.....>>>...<<....>>.
..<<<..>>>..<<<<<...<<<..<<<..((((..(((>>>..>>>...
.>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>
>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<
<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>
>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.>>
..<<<<<<....<.<<<....>>>.><<.<<<<<<<..............
........<<<.<<<<<<<<<...<<<....<<<..<.<<<.........
.>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>>>
>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.
>>>>....<<<......>>>...<<<<<<<...<<<(((.......<<<<
<.....<<..........<<<.<<<<<<<<<<..........<...<...
..................>.........................>.....
>>>>>>>>>>>>>..........))).>>...>>>>>..>>>...>>>>>
>><<<<<<.<<<..........)))..))))...<<...>>.........
.........>>>>>>>>>....>>>>>>.<<<<<<<<<<.<<......<<
<<.<<<<....>>>>>>>>...>>>>>>>>>>.>>.....>>>>>><<<.
...<<.....<<<<<<.......>>>>>>.<<<.....<<<<<.<<...<
<<<<<...<<.....>>.>>>>>>....((<<<<<<...<<....<<<..
..>>>..........<<.<<<<.............>>>>>>......>>.
...>>>..<<<<<........>>>>>))<<<<....<<<<<..<<<<<<<
<....>>>>>>>>..<<<....>>>...<..<<<<<<<...<<<<<<<<<
<<<.<<<<<<<<<<..[[[..>>>>>>....<<<<<.<<<<.<<<<....
.<<<.....>>>.....>>>>>>>>..>>>>>.....<<<<<<<......
.>>>>>>>>>>>...>>>>>>>>>>>>.........>>>>>>>..>....
......>>.>>>.>>>>.>>>..>>.....<<......>>>>>>>.<<<<
.....>>>>..>>>....<<<<.....<<<<<<<.<<.........<...
..<<<<<...............>>>>><<.<<<<<<<<<<<.........
..............>>>>>..>>>>>>.>>............<<<<<<<<
<..<<<.........>>>..<<<<<<<....<<<<.....>>>>......
>>>>>>>...<<..<<<..<<<<<<....<<<.....<<<<....>>>>.
....>>>.>>>>..>>>>><<<<<<.......>>>>>>........<...
........<<<<<.......>>>>>.....>.....>>....>>.>>>>>
>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<<........>>
>>>....<<<<<..<<<.<<......<<<<.<<<<<<..<<<<..<<<<<
<<<<.<<<<<<<<...>>>>>>>>...<<<<<.....<<<<.........
..................<<<<<<<<..>>>>>>>>..>>>>..>>>>>.
...>>>>>>>>>...>>>>...<<<.....>>>..<<<<<<.........
..>>>>>>..<<...<<<<<<<...<<<<<<.......>>>>>>.....<
<.[.(((>>....>>>>>>>...<<<.<<<<<.......>>>>.>>>><<
<<....>>>>>>)))].....<<<<<<<..<<<..)))))).>>>>>>>>
>>.........>>>>..>>>>>>.......<<.<.<.<<<<<<...<<..
.....>>...>>>>>>...>>.>.>.......<<<<<.<<<<<<..<.<.
<<<<<......>>>>>...>.>.<<<.........>>>.....>>>>>..
>...>>>.>>....<<<<<<<....>>>.>>>>....>>..>>>.>>>>>
.....<<<<<<.<..<<<..<.<<<<<.................>>>>>.
><<<<....<<<<....<<.<<<<<<<]]].>>>>>..>>.>>...>>>>
...>>>><<<<<...<<<<<...........>>>>>...>>>>>.>>>..
.>.>>>>>>..<<<<<<<.<<..<<<<....<<<........<<<<<.<<
..>>.>>>>>.......>>>...<<<..<<<<....<<<<.<<<<<<<..
....>>>>>>>>>>>...>>>>..>>>..............>>>>..>>>
>>>>>><<<<<....................<<.<<<<<<<.<<.....<
<<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>.>
>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6xa1 Selective inhibition of human translation termination by a drug-like compound.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): K42 E55 N121 T122 S123 D152 G153 S154 R166 K178 K179 H180 R182 G184 X185 L188 R189 F190 R192 E196 R198 S229 A230 S257 N265 S295 Q296 G315 G386 R414
• Binding residue (residue number reindexed from 1): K32 E45 N111 T112 S113 D142 G143 S144 R156 K168 K169 H170 R172 G174 X175 L178 R179 F180 R182 E186 R188 S219 A220 S247 N255 S285 Q286 G305 G338 R366

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003747 translation release factor activity
• GO:0004045 aminoacyl-tRNA hydrolase activity
• GO:0005515 protein binding
• GO:0008079 translation termination factor activity
• GO:0016149 translation release factor activity, codon specific
• GO:0043022 ribosome binding
• GO:1990825 sequence-specific mRNA binding

Biological Process

• GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
• GO:0002184 cytoplasmic translational termination
• GO:0006412 translation
• GO:0006415 translational termination
• GO:0006449 regulation of translational termination
• GO:0006479 protein methylation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0018444 translation release factor complex
• GO:0022626 cytosolic ribosome

External links

• PDB: RCSB:6xa1, PDBe:6xa1, PDBj:6xa1
• PDBsum: 6xa1
• PubMed: 33009412
• UniProt: P62495|ERF1_HUMAN Eukaryotic peptide chain release factor subunit 1 (Gene Name=ETF1)