Structure of PDB 6w6l Chain L Binding Site BS02

Receptor Information
>6w6l Chain L (length=169) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVR
SFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFG
IQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRIS
KEEAMRWFQQKYDGIILPG
Ligand information
>6w6l Chain t (length=3510) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggaaaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggggcgcgggacaugug
gcguacggaagacccgcuccccggcgccgcucguggggggcccaaguccu
ucugaucgaggcccagcccguggacggugugaggccgguagcggcccccg
gcgcgcgcccgggucuucccggagucggguugcuugggaaugcagcccaa
agcgggugguaaacuccaucuaaggcuaaauaccggcacgagaccgauag
ucaacaaguaccguaagggaaaguugaaaagaacuuugaagagagaguuc
aagagggcgugaaaccguuaagagguaaacgggugggguccgcgcagucc
gcccggaggauucaacccggcggcggguccggccgugucggcggcccggc
ggaucuuucccgggcgggggaccgucccccggaccggcgaccggccgccg
ccgggcgcauuuccaggcggugcgccgcgaccggcuccgggacggcuggg
aaggcccggcggggaagguggcucggggcccccgaguguuacagcccccc
cggcagcagcacucgccgaaucccggggccgagggagagacccgucgccg
cgcucuccccccugggggggccgggccaccccucccacggcgcgaccgcu
cucccagggggcggggcggacuguccccagugcgccccgggcgggucgcg
ccgucgggcccggggggccacgcgcgcgucccccgaagggggggacggcg
gagagcgcacggggucggcggcgacgucggcuacccacccgacccgucuu
gaaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacg
aaagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccga
ggugggaucccgaggccucuccaguccgccgaggggcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcccacgcaguuuuauccgguaaag
cgaaugauuagaggucuuggggccgaaacgaucucaaccuauucucaaac
uuuaaauggguaagaagcccggcucgcuggcguggagccgggguggaaug
cgagugccuagugggccacuuuugguaagcagaacuggcgcugcgggaug
aaccgaacgccggguuaaggcgcccgaugccgacgcucaucagaccccag
aaaagguguugguugauauagacugccgaaucaacuagcccugaaaaugg
auggcgcuggagcgucgggcccauacccggccgucgccggcgucgagagu
ggacgggagcggcggcccggagccccgcggacgcuacgccgcgacgagua
ggagggccgcugcggugagccuugaagccuagggcgcgggcccgggugga
gccgccgcaggugcagaucuuggugguaguagcaaauauucaaacgagaa
cuuugaaggccgaaguggagaaggguuccaugugaacagcaguugaacau
gggucagucgguccugagagaugggcgagcgccguuccgaagggacgggc
gauggccuccguugcccucggccgaucgaaagggagucggguucagaucc
ccgaauccggaguggcggagaugggcgccgcgaggcguccagugcgguaa
cgcgaccgaucccggagaagccggcgggagccccggggagaguucucuuu
ucuuugugaagggcagggcgcccuggaauggguucgccccgagagagggg
cccgugccuuggaaagcgucgcgguuccggcggcguccggugagcucucg
cuggcccuugaaaauccgggggagaggguguaaaucucgcgccgggccgu
acccauauccgcagcaggucuccaaggugaacagccucuggcauguugga
acaauguagguaagggaagucggcaagccggauccguaacuucgggauaa
ggauuggcucuaagggcuggcagccgacuuagaacuggugcggaccaggg
gaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccgcggcgggu
guugacgcgaugugauuucugcccagugcucugaaugucaaagugaagaa
auucaaugaagcgcggguaaacggcgggaguaacuaugacucucuuaagg
uagccaaaugccucgucaucuaauuagugacgcgcaugaauggaugaacg
agauucccacugucccuaccuacuauccagcgaaaccacagccaagggaa
cgggcuuggcggaaucagcggggaaagaagacccuguugagcuugacucu
agucuggcacggugaagagacguuuuuucacugacccggugaggcggggg
ggcgagcccgaggggcucucgcuucuggcgccaagcgcccgcccggccgg
gcgcgacccgcuccggggacagugccagguggggaguuugacuggggcgg
uacaccugucaaacgguaacgcagguguccuaaggcgagcucagggagga
cagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugauuu
ucaguacgaauacagaccgugaaagcggggccucacgauccuucugaccu
uuuggguuuuaagcaggaggugucagaaaaguuaccacagggauaacugg
cuuguggcggccaagcguucauagcgacgucgcuuuuugauccuucgaug
ucggcucuuccuaucauugugaagcagaauucgccaagcguuggauuguu
cacccacuaauagggaacgugagcuggguuuagaccgucgugagacaggu
uaguuuuacccuacugaugauguguuguugccaugguaauccugcucagu
acgagaggaaccgcagguucagacauuugguguaugugcuuggcugagga
gccaauggggcgaagcuaccaucugugggauuaugacugaacgccucuaa
gucagaaucccgcccaggcggaacgauacggcagcgccgcggagccucgg
uuggccucggauagccgguccccgccggggguccggugcggagugcccuu
cguccugggaaaccucgcccgucacgcaccgcacguucguggggaaccug
gcgcuaaaccauucguagacgaccugcuucugggucgggguuucguacgu
agcagagcagcucccucgcugcgaucuauugaaagucagcccucgacaca
aggguuuguc
.........................<<<<<<.....<<....>>......
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...(((((..<<<<<<)))))..]]]........................
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.............................<<<<<<<<..<<<........
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<<.<<<..<<<<..>>>>>>>>>>>..>>....>..........>..>..
>.>>....>>>>.>.>>.....<<<<<<<<.<<<<<<<<<<.<<<.....
...<<<.<<.<<<.......<<<<<<<<.>>>>>>>>........>>>.>
>>>>...........>>>...>>>>>>>>>>...................
......<<<<<<..>>>>>>....<<.......<<...<....<.<<<<<
...<<...>>.<<<<<<<.<<<<....>>>>.>>>>>>>>>>>>.>....
>....>>.........>>..........<<<<<<....>>>>>>......
..............>>>.>>>>>....>>>...>>>>>>>>..<<<<...
.....>>>><<<<<<....<<<<<<<<<<<<<..<<<...<<<<......
..>>>>.....>>>...<<....>>...<<<<<<<......>>>>>>>..
<<<<<..<<<...<.....[[.......>...>>>...>>>>>.<<<<<<
<<<.<<<<......>>>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.
<...<<<<<<.....<<<<<<<<<..<<<....<<<<<<<....>>>>>>
>.....>>>...<<<..<<.<<........>>>>.>>>....>>>>>>>>
>...<<.......>>......>>>>>>......>.>>..<<<<<<....<
.<<<....>>>.><<.<<<<<<<........<<<.<<<<<<<<<...<<<
....<<...<.<<<<..<.<<<.........>>>.>>>>>.>...>>..>
.>>...>>>>>>>....<<<<<<<<.........>>>>>>>>....>>>>
>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<<....
..>>>...<<<<<<<...<<<(((.......<<<<<.....<<.......
...<<<.<<<<<<<<<<............>>>>>>>>>>>>>........
..))).>>...>>>>>..>>>...>>>>>>><<<<<<.<...........
.....]].....<.....>...................>.>>>>>>....
>>>>>>...<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...
>>>>>>>>>>........>>>>>><<<....<<.....<<<<<<......
.>>>>>>.<<<.....<<<<<.<<...<<<<<<...<<.....>>.>>>>
>>....((<<<<<<...<<....<<<....>>>..........<<.<<<<
<<<<<...>>>>>>>>>>>......>>....>>>..<<<<<........>
>>>>))<<<<....<<<<<...<<<<<<<....>>>>>>>...<<<....
>>>...<..<<<<<<<...<<<<<<<<<<<<.<<<<<<<<<<..{{{..>
>>>>>....<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>
>>>..>>>>>.....<<<<<<<.......>>>>>>>>>>>...>>>>>>>
>>>>>.........>>>>>>>..>..........>>.>>>.>>>>.>>>.
.>>.....<<......>>>>>>>.<<<<.....>>>>..>>>....<<<<
.....<<<<<<<.<<.........<.....<<<<<...............
>>>>><<.<<<<<<<<<<<.>>>>>..>>>>>>.>>............<<
<<<<<<<..<<<.........>>>..<<<<<<<....<<<<.....>>>>
......>>>>>>>...<<..<<<..<<<<<<....<<<...<.<<<<...
.>>>>.>...>>>.>>>>..>>>>><<<<<<.......>>>>>>......
..<...........<<<<<.......>>>>>.....>.....>>....>>
.>>>>>>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<<....
....>>>>>....[[[[[..{{{.{{......[[[[.{{[[[[..<<<<<
.<<<<<<<<<.<<<<<<<<<..>>>>>>>>>...<<<<<.....<<<<..
.<.<<...........>>>...............<<<<<<<......>>>
>>>>..>>>>..>>>>>....>>>>>>>>>..>>>>>...<<<.....>>
>..<<<<<<...........>>>>>>..<<...<<<<<<<...<<<<<<.
......>>>>>>.....<<...(((>>....>>>>>>>...<<<..<<<<
.......>>>>..>>><<<<....>>>>>>))).......((((((..((
(..>>>>>>.)))))))))..........]]]]..}}]]]].......<<
.<...<<<<<<...<<.......>>...>>>>>>....>.>.>.......
<<<<<.<<<<<<..<.<.<<<<<......>>>>>.>...>.<<<......
...>>>.....>>>>>..>...>>>.>>....<<<<<<<....>>>.>>>
>....}}..}}}.]]]]].....<<<<<<.<..<<<..<.<<<<<.....
............>>>>>.><<<<....<<<<....<<.<<<<<<<}}}.>
>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>
>>>>...>>>>>.>>>...>.>>>>>>......<<<<<<.<<..<<<..<
..<.............<.<<<<....>>>>.>.............>....
<<<..<<<<........>>>>..>>>..........>...>>>...>>>>
>>>>.<<<<<.<.............>.....<.<<<<<<<.<<.....<<
<<....<<<<<......>>>>>...>>>>....>>....>>>>.>>>.>.
..>>>>>...
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6w6l An ER translocon for multi-pass membrane protein biogenesis.
Resolution3.84 Å
Binding residue
(original residue number in PDB)
C21 N23 C25 S51 Y55 F60 N97 N98 T102 N104 G106 F107 G108 Q110 G127 D129 Y131
Binding residue
(residue number reindexed from 1)
C13 N15 C17 S43 Y47 F52 N89 N90 T94 N96 G98 F99 G100 Q102 G119 D121 Y123
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0003735 structural constituent of ribosome
GO:0005515 protein binding
GO:0008097 5S rRNA binding
GO:0019843 rRNA binding
GO:0031625 ubiquitin protein ligase binding
GO:1990948 ubiquitin ligase inhibitor activity
Biological Process
GO:0000027 ribosomal large subunit assembly
GO:0002181 cytoplasmic translation
GO:0006364 rRNA processing
GO:0006412 translation
GO:0006605 protein targeting
GO:0010628 positive regulation of gene expression
GO:0032092 positive regulation of protein binding
GO:0032435 negative regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0034504 protein localization to nucleus
GO:0042273 ribosomal large subunit biogenesis
GO:0050821 protein stabilization
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1901798 positive regulation of signal transduction by p53 class mediator
GO:1904667 negative regulation of ubiquitin protein ligase activity
GO:2000059 negative regulation of ubiquitin-dependent protein catabolic process
GO:2000435 negative regulation of protein neddylation
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005840 ribosome
GO:0016020 membrane
GO:0022625 cytosolic large ribosomal subunit
GO:0022626 cytosolic ribosome
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome
GO:1990904 ribonucleoprotein complex

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Molecular Function

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:6w6l, PDBe:6w6l, PDBj:6w6l
PDBsum6w6l
PubMed32820719
UniProtP62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)

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