Structure of PDB 8idt Chain L Binding Site BS01

Receptor Information

>8idt Chain L (length=147) Species: 9606 (Homo sapiens)

PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGLHHHRINFDKYHPG
YFGKVGMKHYHLKRNQSFCPTVNLDKLWTLVSEQTRVNAAKNKTGAAPII
DVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKSVGGACVLVA

Ligand information

>8idt Chain 2 (length=3524)

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
ggcacggugaagagacuuuuuucacugacccggugaggcgggggggcgag
ccccgaggggcucucgcuucuggcgccaagcgcccggccgcgcgccggcc
gggcgcgacccgcuccggggacagugccagguggggaguuugacuggggc
gguacaccugucaaacgguaacgcagguguccuaaggcgagcucagggag
gacagaaaccucccguggagcagaagggcaaaagcucgcuugaucuugau
uuucaguacgaauacagaccgugaaagcggggccucacgauccuucugac
cuuuuggguuuuaagcaggaggugucagaaaaguuaccacagggauacuu
guggcggccaagcguucauagcgacgucgcuuugaugucggcucuuccua
ucauugugaagcagaauucaccaagcguuggauuguucacccacuaauag
ggaacgugagcuggguuuagaccgucgugagacagguuaguuuuacccua
cugaugauguguuguugccaugguaauccugcucaguacgagaggaaccg
cagguucagacauuugguguaugugcuuggcugaggagccaauggggcga
agcuaccaucugugggauuaugacugaacgccucuaagucagaaucccgc
ccaggcggaacgauacggcagcgccgcggagccucgguuggccucggaua
gccggucccccgccgggguccggugcggagugcccuucguccugggaaac
ggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcacg
uucguggggaaccuggcgcuaaaccauucguagacgaccugcuucugggu
cgggguuucguacguagcagagcagcucccucgcugcgaucuauugaaag
ucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8idt Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): P2 S3 R4 R6 K7 T8 R9 K10 R12 H14 V15 S16 H17 G18 H19 G20 R21 I22 H25 R26 K27 P29 G30 G31 R32 G33 N34 G36 H39 H40 H41 R42 I43 N44 K47 Y52 F53 G54 K55 G57 M58 K59 H60 Y61 H62 L63 K64 N74 V82 S83 Q85 T86 D102 R105 L112 G113 K114 G115 K116 R131 R132
• Binding residue (residue number reindexed from 1): P1 S2 R3 R5 K6 T7 R8 K9 R11 H13 V14 S15 H16 G17 H18 G19 R20 I21 H24 R25 K26 P28 G29 G30 R31 G32 N33 G35 H38 H39 H40 R41 I42 N43 K46 Y51 F52 G53 K54 G56 M57 K58 H59 Y60 H61 L62 K63 N73 V81 S82 Q84 T85 D101 R104 L111 G112 K113 G114 K115 R130 R131

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003735 structural constituent of ribosome
• GO:0005515 protein binding

Biological Process

• GO:0002181 cytoplasmic translation
• GO:0006412 translation

Cellular Component

• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005783 endoplasmic reticulum
• GO:0005829 cytosol
• GO:0005840 ribosome
• GO:0015934 large ribosomal subunit
• GO:0016020 membrane
• GO:0022625 cytosolic large ribosomal subunit
• GO:0022626 cytosolic ribosome
• GO:1990904 ribonucleoprotein complex

External links

• PDB: RCSB:8idt, PDBe:8idt, PDBj:8idt
• PDBsum: 8idt
• PubMed: 37491604
• UniProt: P46776|RL27A_HUMAN Large ribosomal subunit protein uL15 (Gene Name=RPL27A)