Structure of PDB 8idy Chain o Binding Site BS01

Receptor Information

>8idy Chain o (length=235) Species: 9606 (Homo sapiens)

PHCSRNPVLVRGIGRYSRSAMYSRKAMYKRKYSAALATVTKPVGGDKNGG
TRVVKLRKMPRYYPTEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIIL
TGRHRGKRVVFLKQLASGLLLVTGPLVLNRVPLRRTHQKFVIATSTKIDI
SNVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEKEKYEITEQRKIDQKAV
DSQILPKIKAIPQLQGYLRSVFALTNGIYPHKLVF

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): H43 C44 S45 R46 N47 P48 R52 Y57 S58 R59 S60 M62 Y63 S64 R65 K66 Y69 K70 R71 Y73 L89 A90 K94 P95 G97 D99 K100 N101 R105 V107 K108 R110 K111 P113 R114 Y115 V121 P122 R123 K124 L125 L126 H128 K130 P132 F133 S134 H136 T154 R156 R158 L172 L179 V180 L181 R183 P185 R187 R188 H190 K192 F217 K219 K221 K224 F233 Y240 I242 K247 K262 P265 Q266 R272 N279
• Binding residue (residue number reindexed from 1): H2 C3 S4 R5 N6 P7 R11 Y16 S17 R18 S19 M21 Y22 S23 R24 K25 Y28 K29 R30 Y32 L36 A37 K41 P42 G44 D46 K47 N48 R52 V54 K55 R57 K58 P60 R61 Y62 V68 P69 R70 K71 L72 L73 H75 K77 P79 F80 S81 H83 T101 R103 R105 L119 L126 V127 L128 R130 P132 R134 R135 H137 K139 F164 K166 K168 K171 F180 Y187 I189 K194 K209 P212 Q213 R219 N226

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding
• GO:0045296 cadherin binding

Biological Process

• GO:0000027 ribosomal large subunit assembly
• GO:0002181 cytoplasmic translation
• GO:0006355 regulation of DNA-templated transcription
• GO:0006412 translation

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005791 rough endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0005925 focal adhesion
• GO:0014069 postsynaptic density
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:0036464 cytoplasmic ribonucleoprotein granule
• GO:0045202 synapse
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8idy, PDBe:8idy, PDBj:8idy
• PDBsum: 8idy
• PubMed: 37491604
• UniProt: Q02878|RL6_HUMAN Large ribosomal subunit protein eL6 (Gene Name=RPL6)