Structure of PDB 8a3d Chain q Binding Site BS01

Receptor Information

>8a3d Chain q (length=170) Species: 9606 (Homo sapiens)

KENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTV
RSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGF
GIQEHIDLGIKYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRI
SKEEAMRWFQQKYDGIILPG

Ligand information

>8a3d Chain A (length=3303)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccggggggcccaaguccuucugaucgaggcccag
cccguggacggugugaggccgguagcggcccccggccgggucuucccgga
gucggguugcuugggaaugcagcccaaagcgggugguaaacuccaucuaa
ggcuaaauaccggcacgagaccgauagucaacaaguaccguaagggaaag
uugaaaagaacuuugaagagagaguucaagagggcgugaaaccguuaaga
gguaaacgggugggguccgcgcaguccgcccggaggauucaacccggcgg
cggguccggccgggcggaucugaccgucggcgaccggccgccgccgggcg
cauuuccaccgcggcggugcgccgcgaccggcuccgggacggcugggaag
gcccggcggggaagguggcucggccgaguguuacagcccccccggcagca
gcacucgccgaaucccggggccgagggaggucgccgcgcucuccccccug
ggggggccgggccaccccucccacggcgcgaccgcucggggcggacuguc
cccagugcgccccgggcgggucgcgccgucgggcccggggggccacgcgc
gcgucccgggacggcggagcgagcgcacggggucggcggcgacgucggcu
acccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgc
gagucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggcc
ggccgaggugggaucccgaggccucucgccgagggcgcaccaccggcccg
ucucgcccgccgcgccggggagguggagcacgagcgcacguguuaggacc
cgaaagauggugaacuaugccugggcagggcgaagccagaggaaacucug
guggagguccguagcgguccugacgugcaaaucggucguccgaccugggu
auaggggcgaaagacuaaucgaaccaucuaguagcugguucccuccgaag
uuucccucaggauagcuggcgcucucggcaguuuuauccgguaaagcgaa
ugauuagagguaccuauucucaaacuuuaaauggguaagaagcccggcuc
gcuggcguggagccgggcguggaaugcgagugccuagugggccacuuuug
guaagcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcc
cgaugccgacgcucaucagaccccagaaaagguguugguugauauagaca
ggaaucaacuagcccugaaaauggauggcgcuggagcgucgggcccauac
ccggccgucgccggcaguccgcggacgcuacgccgcgacgaguaggaggg
ccgcugcggugagccuugaagccuagggcgcgggcccggguggagccgcc
gcaggugcagaucuuggugguaguagcaaauauucaaacgagaacuuuga
aggccgaaguggagaaggguuccaugugaacagcaguugaacauggguca
gucgguccugagagaugggcgagcgccguuccgaagggggccgaucgaaa
gggagucggguucagauccccgaauccggagcggagaugggcgccgcgag
gcguccagugcgguaacgcgaccgaucccggagaagccggcgggagcccc
ggggagaguucucuuuucuuugugaagggcagggcgcccuggaauggguu
cgccccgagagaggggcccgugccuuggaaagcgucgcgguuccggcggc
guccggugagcucucgcuggcccuugaaaauccgggggagaggguguaaa
ucucgcgccgggccguacccauauccgcagcaggucuccaaggugaacag
ccucuggcauguuggaacaauguagguaagggaagucggcaagccggauc
cguaacuucgggauaaggauuggcucuaagggcuagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgggagcucucuu
aagguagccaaaugccucgucaucuaauuagugacgcgcaugaauggaug
aacgagauucccacugucccuaccuacuauccagcgaaaccacagccaag
ggaacgggcuuggcggaaucagcggggaaagaagacccuguugagcuuga
cucuagucuggcacggugaagaguuuuucacugacccggugaggcggggg
gcgcuucuggcgccaagcgcccggccgggcgcgacccgcuccggggacag
ugccagguggggaguuugacuggggcgguacaccugucaaacgguaacgc
agguguccuaaggcgagcucagggaggacagaaaccucccguggagcaga
agggcaaaagcucgcuugaucuugauuuucaguacgaauacagaccguga
aagcggggccucacgauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcguucau
agcgacgucgcuuuuugauccuucgaugucggcucuuccuaucauuguga
agcagaauucaccaagcguuggauuguucacccacuaauagggaacguga
gcuggguuuagaccgucgugagacagguuaguuuuacccuacugaugaug
uguuguugccaugguaauccugcucaguacgagaggaaccgcagguucag
acauuugguguaugugcuuggcugaggagccaauggggcgaagcuaccau
cugugggauuaugacugaacgccucuaagucagaaucccgcccaggcgga
acgauacggcagcgccgcggagccucgguuggccucggauagccgguccc
cgggguccggugcggagugcccuucguccugggaaacggggcgcggccgg
aaaggcggccgcccccucgcccgucacgcaccgcacguucguggggaacc
uggcgcuaaaccauucguagacgaccugcuugggucgggguuucguacgu
agcagagcagcgcugcgaucuauugaaagucagcccucgacacaaggguu
ugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8a3d The chemical landscape of the human ribosome at 1.67 angstrom resolution.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): K19 C21 N23 C25 G27 S51 A53 R54 V57 S59 F60 I62 H71 N97 N98 S100 D101 T102 N104 G106 F107 G108 G127 L128 D129 Y131 K145
• Binding residue (residue number reindexed from 1): K12 C14 N16 C18 G20 S44 A46 R47 V50 S52 F53 I55 H64 N90 N91 S93 D94 T95 N97 G99 F100 G101 G120 L121 D122 Y124 K138

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

External links

• PDB: RCSB:8a3d, PDBe:8a3d, PDBj:8a3d
• PDBsum: 8a3d
• PubMed: 36909531
• UniProt: P62913|RL11_HUMAN Large ribosomal subunit protein uL5 (Gene Name=RPL11)