Structure of PDB 8idy Chain V Binding Site BS01

Receptor Information

>8idy Chain V (length=201) Species: 9606 (Homo sapiens)

EVQVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKL
KYLAFLRKRMNTNPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRL
KVFDGIPPPYDKKKRMVVPAALKVVRLKPTRKFAYLGRLAHEVGWKYQAV
TATLEEKRKEKAKIHYRKKKQLMRLRKQAEKNVEKKIDKYTEVLKTHGLL
V

Ligand information

>8idy Chain 2 (length=3641)

cgcgaccucagaucagacguggcgacccgcugaauuuaagcauauuaguc
agcggaggagaagaaacuaaccaggauucccucaguaacggcgagugaac
agggaagagcccagcgccgaauccccgccccgcggcggggcgcgggacau
guggcguacggaagacccgcuccccggcgccgcucguggggggcccaagu
ccuucugaucgaggcccagcccguggacggugugaggccgguagcggccc
ccggcgcgccgggcccgggucuucccggagucggguugcuugggaaugca
gcccaaagcgggugguaaacuccaucuaaggcuaaauaccggcacgagac
cgauagucaacaaguaccguaagggaaaguugaaaagaacuuugaagaga
gaguucaagagggcgugaaaccguuaagagguaaacgggugggguccgcg
caguccgcccggaggauucaacccggcggcggguccggccgugucggcgg
cccggcggaucuuucccgcgcgggggaccgucccccgaccggcgaccggc
cgccgccgggcgcauuuccaccgcggcggugcgccgcgaccggcuccggg
acggcugggaaggcccggcggggaagguggcucgggggcccccgaguguu
acagcccccccggcagcagcacucgccgaaucccggggccgagggagcga
gacccgucgccgcgcucuccccccucccggcgcgccggggggggccgggc
caccccucccacggcgcgaccgcucggggcggacuguccccagugcgccc
cgggcgggucgcgccgucgggcccgggggaggccacgcgcgcgucccccg
aagagggggacggcggagcgagcgcacggggucggcggcgacgucggcua
cccacccgacccgucuugaaacacggaccaaggagucuaacacgugcgcg
agucgggggcucgcacgaaagccgccguggcgcaaugaaggugaaggccg
gcgcgcucgccggccgaggugggaucccgaggccucuccaguccgccgag
ggcgcaccaccggcccgucucgcccgccgcgccggggagguggagcacga
gcgcacguguuaggacccgaaagauggugaacuaugccugggcagggcga
agccagaggaaacucugguggagguccguagcgguccugacgugcaaauc
ggucguccgaccuggguauaggggcgaaagacuaaucgaaccaucuagua
gcugguucccuccgaaguuucccucaggauagcuggcgcucucgcagacc
cgacgcccgccacgcaguuuuauccgguaaagcuuuaaauggguaagaag
cccggcucgcuggcguggagccgggcguggaaugcgagugccuagugggc
cacuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguu
aaggcgcccgaugccgacgcucaucagaccccagaaaagguguugguuga
uauagacagcaggacgguggccauggaagucggaauccgcuaaggagugu
guaacaacucaccugccgaaucaacuagcccugaaaauggauggcgcugg
agcgucgggcccauacccggccgucgccggcagucgagaguggacgggag
cggcggcccggagccccgcggacgcuacgccgcgacgaguaggagggccg
cugcggugagccuugaagccuagggcgcgggcccggguggagccgccgca
ggugcagaucuuggugguaguagcaaauauucaaacgagaacuuugaagg
ccgaaguggagaaggguuccaugugaacagcaguugaacaugggucaguc
gguccugagagaugggcgagcgccguuccgaagggacgggcgauggccuc
cguugcccucggccgaucgaaagggagucggguucagauccccgaauccg
gaguggcggagaugggcgccgcgaggcguccagugcgguaacgcgaccga
ucccggagaagccggcgggagccccggggagaguucucuuuucuuuguga
agggcagggcgcccuggaauggguucgccccgagagaggggcccgugccu
uggaaagcgucgcgguuccggcggcguccggugagcucucgcuggcccuu
gaaaauccgggggagaggguguaaaucucgcgccgggccguacccauauc
cgcagcaggucuccaaggugaacagccucuggcauguuggaacaauguag
guaagggaagucggcaagccggauccguaacuucgggauaaggauuggcu
cuaagggcugggucggucgcggccggcgccuagcagccgacuuagaacug
gugcggaccaggggaauccgacuguuuaauuaaaacaaagcaucgcgaag
gcccgcggcggguguugacgcgaugugauuucugcccagugcucugaaug
ucaaagugaagaaauucaaugaagcgcggguaaacggcgugaacgagauu
cccacugucccuaccuacuauccagcgaaaccacagccaagggaacgggc
uuggcggaaucagcggggaaagaagacccuguugagcuugacucuagucu
ggcacggugaagagacaugagagguguagaauaagugggaggcccccggc
gcccccccgguguccccgcgaggggcccggggcgggguccgccggcccug
cgggccgccggugaaauaccacuacucugaucguuuuuucacugacccgg
ugaggcgggggggcgagccccgaggggcucucgcuucuggcgccaagcgc
ccggccgcgcgccggccgggcgcgacccgcuccggggacagugccaggug
gggaguuugacuggggcgguacaccugucaaacgguaacgcagguguccu
aaggcgagcucagggaggacagaaaccucccguggagcagaagggcaaaa
gcucgcuugaucuugauuuucaguacgaauacagaccgugaaagcggggc
cucacgauccuucugaccuuuuggguuuuaagcaggaggugucagaaaag
uuaccacagggauacuuguggcggccaagcguucauagcgacgucgcuuu
gaugucggcucuuccuaucauugugaagcagaauucaccaagcguuggau
uguucacccacuaauagggaacgugagcuggguuuagaccgucgugagac
agguuaguuuuacccuacugaugauguguuguugccaugguaauccugcu
caguacgagaggaaccgcagguucagacauuugguguaugugcuuggcug
aggagccaauggggcgaagcuaccaucugugggauuaugacugaacgccu
cuaagucagaaucccgcccaggcggaacgauacggcagcgccgcggagcc
ucgguuggccucggauagccggucccccgccgggguccggugcggagugc
ccuucguccugggaaacggggcgcggccggagaggcggccgcccccucgc
ccgucacgcaccgcacguucguggggaaccuggcgcuaaaccauucguag
acgaccugcuucugggucgggguuucguacguagcagagcagcucccucg
cugcgaucuauugaaagucagcccucgacacaaggguuugu

.........................<<<<<<<....<<....>>.....>
>>>>>.>.........<<....>>..<<<<<<.....<<.....>>....
>>>>>>..[[[..<<<<<...<<<<<<<<<<.....>>>>>>.>>>>...
..>>>>>..<<<<<<<<<<...<<.<<<<<........<<<<<<<<....
<<<<......>>>>.....((......<<<.....))>>>...>.>>>>>
>>...>>>>>.>>..>>>>>>>>>>.......<<<<<<<........>>>
>>>>.....(((((..<<<<<<)))))..]]]..................
................<<....>>...............<<<......>>
>..................................<<<<<<<<..<<<.<
<...<<<<<<<<.<<<.....<<<<<<<<<<<..<<<<<<<..<....<<
....<<<<.<<<..<<......>>>>>>>>>>>...>..>>>>...>>>>
>>>>>>>>>>......>>>.>>>.>>>>>...<<<<<<<<<<<<<<<<<<
<<<<<...<<..<<<....<<<<......<<<<<<<<..>>>>>>>>...
....>>>>...>>>........>>>>>>..>>>>>>>>>>>.........
...........<<<<<..<<<<<<<............>>>>>>>.<<<<<
<.<<<<.<<<<<<<<<<.<<<<<<.<<<<..<...........>...>>>
>.>>>>>.>.>>>>>>>.>>>...>>>>..>>>>.>>..<<<<<<<<<..
.....>>>>>>>.>>.....>>>>>.....>>>.>>>>>...>>>>>...
>>>>>>>>..<<<<........>>>><<<<<<....<<<<<<<<<<<<<.
.<<<...<<<<........>>>>.....>>>...<<....>>...<<<<<
<<......>>>>>>>..<<<<<...<<<..<<<..[[....(((>>>..>
>>....>>>>>.<<<<<<<<<.<<<<......>>>>>>>>>>>.>>....
>>>>>>>>>>>>>..<<.<..<<<<<<<.....<<<<<<<<<..<<<...
.<<<<<<<....>>>>>>>.....>>>...<<<..<<.<<........>>
>>.>>>....>>>>>>>>>...<<.......>>......>>>>>>...>.
.>.>>..<<<<<<....<.<<<....>>>.><<<<<<<<<<.........
.............<<<.<<<<<<<<....<<...>>....>>>>>>...<
<<<<<<<<.<......>>>>>>>>>>....>>>>>>>>>>>>.>>>..<<
<<.<<<<<.....>>>>>.>>>>....<<<......>>>...<<<<<<<.
..<<<(((.......<<<<<.....<<..........<<<.<<<<<<<<<
<.......<<<<<.<<....<<.........>>....>>.........<<
......>>...>>>>>...>>>>>>>>>>>>>..........))).>>..
.>>>>>..>>>...>>>>>>><<<<<<.<<<..........)))....]]
............................>>>>>>>>>....>>>>>>.<<
<<<<<<<<.<<......<<<<.<<<<....>>>>>>>>...>>>>>>>>>
>.>>.....>>>>>><<<....<<.....<<<<<<.......>>>>>>.<
<<.....<<<<<.<<...<<<<<....<<.....>>..>>>>>....((<
<<<<<...<<....<<<....>>>..........<<.<<<<<..<<...>
>..>>>>>>>......>>....>>>..<<<<<........>>>>>))<<<
<....<<<<<..<<<<<.<<....>>.>>>>>..<<<....>>>...<..
<<<<<<<...<<<<<<<<<<<<<<<<<<<<<<<..{{{..>>>>>>....
<<<<<.<<<<.<<<<.....<<<.....>>>.....>>>>>>>>..>>>>
>.....<<<<<<<.......>>>>>>>>>>>.>.>>>>>>>>>>>>....
.....>>>>>>>..>..........>>.>>>.>>>>.>>>..>>.....<
<......>>>>>>>.<<<<.....>>>>..>>>....<<<<.....<<<<
<<<.<<.........<.....<<<<<.....<..>......>>>>><<.<
<<<<<<<<<<.......................>>>>>..>>>>>>.>>.
...........<<<<<<<<<..<<<.........>>>..<<<<<<<....
<<<<.....>>>>......>>>>>>>.......<<<..<<<<<.<...<<
<.....<<<<....>>>>.....>>>.>>>>..>>>>>.....>>.>>>>
>>>..>..>>.>>>>>>>..>>>>>>...>>>....<<<<<........>
>>>>....[[[[[..{{{........[[[[[.{{[[[[..<<<<<.<<<<
<<<<<.<<<<<<.<....................................
....<<.........<.....>......>>....................
..................................>.>>>>>>...<<<<<
.....<<<<........<<....>>.....................<<<<
<<<<<<.......>>>>>>>>>>..>>>>..>>>>>....>>>>>>>>>.
.>>>>>...<<<.....>>>.<<<<<<<...........>>>>>>>.<<.
..<<<<<<<...<<<<<<.......>>>>>>.....<<.[.(((>>....
>>>>>>>...<<<.<<<<<.......>>>>.>>>>.<<<....>>>.>>)
))]......((((((..(((..>>>>>>.)))))))))..........]]
]]..}}]]]]]........<<<<<<...<<.......>>...>>>>>>..
((...<<<<.<<<<<<..<.<.<<<<<......>>>>>...>.>.<<<..
...))..>>>.....>>>>>..>...>>>>......<<<<<<<....>>>
.>>>>........}}}.]]]]].....<<<<<<.<..<<<..<.<<<<<.
................>>>>>.><<<<....<<<<....<<.<<<<<<<}
}}.>>>>>..>>.>>...>>>>...>>>><<<<<...<<<<<........
...>>>>>...>>>>>.>>>...>.>>>>>>.....<<<<<<..<<..<<
<<....<<<........<<<<<.<<<<....>>>>.>>>>>.......>>
>...<<<..<<<<....<<<<.<<<<<<<......>>>>>>>>>>>...>
>>>..>>>..............>>>>..>>.>>>>>><<<<<.<......
.......>....<<.<<<<<<<.<<.....<<<<.<..<<<<<......>
>>>>..>>>>>....>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8idy Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): R12 G17 R18 K25 L28 R37 S44 Y48 R49 L55 K60 R61 M62 N63 N65 R68 Y71 H72 F73 R74 T83 R85 M87 P89 H90 K93 R94 F105 D106 I108 P110 D113 K114 K115 K116 R128 L129 K130 R133 E144 V145 K148 Y149 L156 K159 K163 K165 H167 Y168 R169 K171 K172 M175 R176 K188 L202 V203
• Binding residue (residue number reindexed from 1): R10 G15 R16 K23 L26 R35 S42 Y46 R47 L53 K58 R59 M60 N61 N63 R66 Y69 H70 F71 R72 T81 R83 M85 P87 H88 K91 R92 F103 D104 I106 P108 D111 K112 K113 K114 R126 L127 K128 R131 E142 V143 K146 Y147 L154 K157 K161 K163 H165 Y166 R167 K169 K170 M173 R174 K186 L200 V201

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003729 mRNA binding
• GO:0003735 structural constituent of ribosome

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation
• GO:0006417 regulation of translation
• GO:0017148 negative regulation of translation
• GO:0032496 response to lipopolysaccharide
• GO:0042592 homeostatic process
• GO:0048246 macrophage chemotaxis
• GO:0060425 lung morphogenesis
• GO:0071346 cellular response to type II interferon
• GO:1901194 negative regulation of formation of translation preinitiation complex

Cellular Component

• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0045202 synapse
• GO:0097452 GAIT complex
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8idy, PDBe:8idy, PDBj:8idy
• PDBsum: 8idy
• PubMed: 37491604
• UniProt: P40429|RL13A_HUMAN Large ribosomal subunit protein uL13 (Gene Name=RPL13A)