Structure of PDB 6xa1 Chain LG Binding Site BS01

Receptor Information

>6xa1 Chain LG (length=241) Species: 9606 (Homo sapiens)

KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLK
VPPAINQFTQALDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGK
GDVPTKRPPVLRAGVNTVTTLVENKKAQLVVIAHDVDPIELVVFLPALCR
KMGVPYCIIKGKARLGRLVHRKTCTTVAFTQVNSEDKGALAKLVEAIRTN
YNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKLG

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

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

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): E33 K34 R35 K37 F39 I41 Q43 I45 Q46 P47 L51 R53 F54 V55 K56 P58 R59 Y60 K72 R73 L74 K75 E105 K110 K111 R113 R132 G139 V140 N141 T142 T145 V161 D162 L166 K187 A188 R196 K197 T198 T200 P244 K245 S246 R249
• Binding residue (residue number reindexed from 1): E8 K9 R10 K12 F14 I16 Q18 I20 Q21 P22 L26 R28 F29 V30 K31 P33 R34 Y35 K47 R48 L49 K50 E80 K85 K86 R88 R107 G114 V115 N116 T117 T120 V136 D137 L141 K162 A163 R171 K172 T173 T175 P219 K220 S221 R224

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000470 maturation of LSU-rRNA
• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0042254 ribosome biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:6xa1, PDBe:6xa1, PDBj:6xa1
• PDBsum: 6xa1
• PubMed: 33009412
• UniProt: P62424|RL7A_HUMAN Large ribosomal subunit protein eL8 (Gene Name=RPL7A)