Structure of PDB 8glp Chain LD Binding Site BS01

Receptor Information

>8glp Chain LD (length=294) Species: 9606 (Homo sapiens)

GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRM
IVRVTNRDIICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCT
GLLLARRLLNRFGMDKIYEGQVEVTGDEYNVESIDGQPGAFTCYLDAGLA
RTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVHRKHIMG
QNVADYMRYLMEEDEDAYKKQFSQYIKNSVTPDMMEEMYKKAHAAIRENP
VYEKKPKKEVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAA

Ligand information

>8glp Chain L5 (length=3546)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgc
ggcggaucuuucccggcgggggaccgucccccgaccggcgaccggccgcc
gccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccgggacgg
cugggaaggcccggcggggaagguggcucgggggcccccgaguguuacag
cccccccggcagcagcacucgccgaaucccggggccgagggagcgagacc
cgucgccgcgcucuccccccugggggggccgggccaccccucccacggcg
cgaccgcucggggcggacuguccccagugcgccccgggcgggucgcgccg
ucgggcccggggggccacgcgcgcgucccccgaagagggggacggcggag
cgagcgcacggggucggcggcgacgucggcuacccacccgacccgucuug
aaacacggaccaaggagucuaacacgugcgcgagucgggggcucgcacga
aagccgccguggcgcaaugaaggugaaggccggcgcgcucgccggccgag
gugggaucccgaggccucuccaguccgccgagggcgcaccaccggcccgu
cucgcccgccgcgccggggagguggagcacgagcgcacguguuaggaccc
gaaagauggugaacuaugccugggcagggcgaagccagaggaaacucugg
uggagguccguagcgguccugacgugcaaaucggucguccgaccugggua
uaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaagu
uucccucaggauagcuggcgcucucgcagacccgagccacgcaguuuuau
ccgguaaagcgaaugauuagaggucuuggggccgaaacgaucucaaccua
uucucaaacuuuaaauggguaagaagcccggcucgcuggcguggagccgg
gcguggaaugcgagugccuagugggccacuuuugguaagcagaacuggcg
cugcgggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucau
cagaccccagaaaagguguugguugauauagacagcaggaaccugccgaa
ucaacuagcccugaaaauggauggcgcuggagcgucgggcccauacccgg
ccgucgccggcagucgagaguggacgggagccccgcggacgcuacgccgc
gacgaguaggagggccgcugcggugagccuugaagccuagggcgcgggcc
cggguggagccgccgcaggugcagaucuuggugguaguagcaaauauuca
aacgagaacuuugaaggccgaaguggagaaggguuccaugugaacagcag
uugaacaugggucagucgguccugagagaugggcgagcgccguuccgaag
ggacgggcgauggccuccguugcccucggccgaucgaaagggagucgggu
ucagauccccgaauccggagcggagaugggcgccgcgaggcguccagugc
gguaacgcgaccgaucccggagaagccggcgggagccccggggagaguuc
ucuuuucuuugugaagggcagggcgcccuggaauggguucgccccgagag
aggggcccgugccuuggaaagcgucgcgguuccggcggcguccggugagc
ucucgcuggcccuugaaaauccgggggagaggguguaaaucucgcgccgg
gccguacccauauccgcagcaggucuccaaggugaacagccucuggcaug
uuggaacaauguagguaagggaagucggcaagccggauccguaacuucgg
gauaaggauuggcucuaagggcugguagcagccgacuuagaacuggugcg
gaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaaggcccg
cggcggguguugacgcgaugugauuucugcccagugcucugaaugucaaa
gugaagaaauucaaugaagcgcggguaaacggcgggaguaacuaugacuc
ucuuaagguagccaaaugccucgucaucuaauuagugacgcgcaugaaug
gaugaacgagauucccacugucccuaccuacuauccagcgaaaccacagc
caagggaacgggcuuggcggaaucagcggggaaagaagacccuguugagc
uugacucuagucuggcacggugaagagacguuuuuucacugacccgguga
ggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgcccg
gccgcgcgccggccgggcgcgacccgcuccggggacagugccaggugggg
aguuugacuggggcgguacaccugucaaacgguaacgcagguguccuaag
gcgagcucagggaggacagaaaccucccguggagcagaagggcaaaagcu
cgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggccuc
acgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguua
ccacagggauaacuggcuuguggcggccaagcguucauagcgacgucgcu
uuuugauccuucgaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggguuuaga
ccgucgugagacagguuaguuuuacccuacugaugauguguuguugccau
gguaauccugcucaguacgagaggaaccgcagguucagacauuuggugua
ugugcuuggcugaggagccaauggggcgaagcuaccaucugugggauuau
gacugaacgccucuaagucagaaucccgcccaggcggaacgauacggcag
cgccgcggagccucgguuggccucggauagccggucccccgcgggguccg
gugcggagugcccuucguccugggaaacggggcgcggccggagaggcggc
cgcccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaa
accauucguagacgaccugcuucugggucgggguuucguacguagcagag
cagcgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8glp mRNA decoding in human is kinetically and structurally distinct from bacteria.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): G2 F3 K5 K8 K10 A11 R15 Y16 Q17 K19 R23 G26 T28 Y31 R35 L36 K43 Y44 T46 K48 Y49 F113 M115 P139 G140 F142 Y145 L150 R152 T153 F160 P174 H175 S176 R179 R268 S272 A274 Q275 D278 R279 Q282 S286 F287 R289 A290
• Binding residue (residue number reindexed from 1): G1 F2 K4 K7 K9 A10 R14 Y15 Q16 K18 R22 G25 T27 Y30 R34 L35 K42 Y43 T45 K47 Y48 F112 M114 P138 G139 F141 Y144 L149 R151 T152 F159 P173 H174 S175 R178 R267 S271 A273 Q274 D277 R278 Q281 S285 F286 R288 A289

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003730 mRNA 3'-UTR 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:0048027 mRNA 5'-UTR 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:0010628 positive regulation of gene expression
• GO:0042273 ribosomal large subunit biogenesis
• GO:0045727 positive regulation of translation
• GO:0050821 protein stabilization
• GO:1901796 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:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• 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

External links

• PDB: RCSB:8glp, PDBe:8glp, PDBj:8glp
• PDBsum: 8glp
• PubMed: 37020024
• UniProt: P46777|RL5_HUMAN Large ribosomal subunit protein uL18 (Gene Name=RPL5)