Structure of PDB 6xa1 Chain Lb Binding Site BS01

Receptor Information

>6xa1 Chain Lb (length=109) Species: 9606 (Homo sapiens)

AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNK
KGLKKMQANNAKAMSARAEAIKALVASRKLDRLAYIAHPKLGKRARARIA
KGLRLCRPK

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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>>>..<<<<<<<<<<...<<..<<<<<<<<....<<<<......>>>>.(
(......<<<.....))>>>...>.>>>>>>>.>>..>>>>>>>>>>...
....<<<<<<<........>>>>>>>.....<<<<<..((((((>>>>>.
.>>>..................................<<....>>....
...........<<<<....>>>>...........................
.......<<<<<<<<..<<<.<<...<<<<<<<<.<<<.....<<<<<<<
<<<<..<<<....<<<<<.<<<.>>>>>>>>..>>>>>>>>>>>>>>...
...>>>.>>>.>>>>>...<<<<<<<.<<<<<<<<<<.<<<<...<<..<
<<....<<<<......<<<<<..>>>>>.......>>>>...>>>.....
...>>>>>>...>>>>>>>>>>....................<<<<<<.<
<<<<<..>>>>>>.<<<<<<.<<<<.<<<<<<<<<<<.<<<<<<<<<<<.
<<<<....>>>>.>>>>>>>.>>>>.>.>>>>>>>.>>>...>>>>>>>>
.>>..<<<<<<<..>>>>>.>>....>>>>>>......>>.>>>>>...>
>>>>...>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<
<<<<<<..<<<...<<<<........>>>>.....>>>...<<....>>.
..<<<..>>>..<<<<<...<<<..<<<..((((..(((>>>..>>>...
.>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....>>>>>
>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<....<<<<
<<<....>>>>>>>.....>>>...<<<..<<.<<........>>>>.>>
>....>>>>>>>>>...<<.......>>......>>>>>>...>..>.>>
..<<<<<<....<.<<<....>>>.><<.<<<<<<<..............
........<<<.<<<<<<<<<...<<<....<<<..<.<<<.........
.>>>.>..>>>..>.>>...>>>>>>>...<<<<<<<<<.<......>>>
>>>>>>>....>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.
>>>>....<<<......>>>...<<<<<<<...<<<(((.......<<<<
<.....<<..........<<<.<<<<<<<<<<..........<...<...
..................>.........................>.....
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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): A2 K3 K5 N6 H7 T8 T9 H10 N11 S13 R14 K15 H17 R18 N19 R25 Q27 R28 Y29 S31 L32 K33 D36 R41 N42 R44 F45 A46 K47 H49 N50 K52 K56 M57 N61 S90 R91 K92 R95 Y98 H101 P102 K103 R107 R111 K114 G115 R117 L118 R120 P121 K122
• Binding residue (residue number reindexed from 1): A1 K2 K4 N5 H6 T7 T8 H9 N10 S12 R13 K14 H16 R17 N18 R24 Q26 R27 Y28 S30 L31 K32 D35 R40 N41 R43 F44 A45 K46 H48 N49 K51 K55 M56 N60 S77 R78 K79 R82 Y85 H88 P89 K90 R94 R98 K101 G102 R104 L105 R107 P108 K109

Gene Ontology

Molecular Function

• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0006412 translation

Cellular Component

• GO:0005840 ribosome

External links

• PDB: RCSB:6xa1, PDBe:6xa1, PDBj:6xa1
• PDBsum: 6xa1
• PubMed: 33009412
• UniProt: P47914|RL29_HUMAN Large ribosomal subunit protein eL29 (Gene Name=RPL29)