Structure of PDB 6xa1 Chain Lr Binding Site BS01

Receptor Information

>6xa1 Chain Lr (length=125) Species: 9606 (Homo sapiens)

SAHLQWMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGV
EPAADGKGVVVVIKRRSGQRKPATSYVRTTINKNARATLSSIRHMIRKNK
YRPDLRMAAIRRASAILRSQKPVMV

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): W7 R11 N12 S15 K19 R20 K22 T24 K33 R35 N36 S37 F38 R39 R66 R67 S68 T80 K84 N85 R87 S92 H95 R98 K99 N100 D105 R107 M108 R112
• Binding residue (residue number reindexed from 1): W6 R10 N11 S14 K18 R19 K21 T23 K32 R34 N35 S36 F37 R38 R65 R66 S67 T79 K83 N84 R86 S91 H94 R97 K98 N99 D104 R106 M107 R111

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0030425 dendrite
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0044297 cell body
• GO:0045202 synapse
• GO:0070062 extracellular exosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xa1, PDBe:6xa1, PDBj:6xa1
• PDBsum: 6xa1
• PubMed: 33009412
• UniProt: P46779|RL28_HUMAN Large ribosomal subunit protein eL28 (Gene Name=RPL28)