Structure of PDB 8fkw Chain SZ Binding Site BS02

Receptor Information

>8fkw Chain SZ (length=160) Species: 9606 (Homo sapiens)

PKAKGKTRRQKFGYSVNRKRLNRNARRKAAPRIECSHIRHAWDHAKSVRQ
NLAEMGLAVDPNRAVPLRLVRKPYVLNDLEAEASLPEKKGNTLSRDLIDY
VRYMVENHGEDYKAMARDEKNYYQDTPKQIRSKINVYKRFYPAEWQDFLD
SLQKRKMEVE

Ligand information

>8fkw Chain L3 (length=2277)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcg
ccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcuc
gggcccgaguguuacagcccccccggcagcagcacucgccgaaucccggg
gccgagggagcgccgcgcucuccggccgggccaggccacggagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuugaaacacggacc
aaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgug
gcgcaaggugggaucccgaggcccgccgagggcgcaccaccggcccgucu
cgcccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaaaccaucuaguagcugguucccuccgaaguuucccggauagcuggcgc
ucuccgcaguuuuauccgguggguaagaagcccggcucgagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucacgcuacgccgcgacgaguaggagggccgcugcggugagccuug
aagccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggu
gguaguagcauucaaacgagaacuuugaaggccgaaguggagaaggggcg
auggccuccggcccucgcggagaugggcgccgcgaggcguccagugaauc
ucgcccgcagcaggucuccggugaacagccucuggcaauguagguaaggg
aagucgggaauccgauucccacugucccuaccuacuauccagcgaaacca
cagccaagggaacgggcuuggcggaaucagcggggagaagacccuguuga
gcuugacucuagucuggcacggugaagagacaugagagguguagaauaag
ugggaggcggccgccggugaaauaccacuacucugaucguuuuuuccagu
gccagguggggaguuauccuucugaccuuuuggguuuuaagcaggaggug
ucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgcgacg
ucgcuuuuugaugaugucggcucuuccuaucauugugaagcagaauucac
caagcguuggauuguucacccacuaauagggaacgugagcuggggaccgu
cgugagacagguucccuacugaugguuguugccaugguaauccugcucag
uacgagaggaaccgcagguucagacauuugguggugcuuggcugaggagc
caauggggcgaagcuaccaucugugggauuaugacugaacgccucuaagu
cagaaucccgcccaggcggaacgauaagcgccgcggagccucgguuggcc
ucggauagccgguccccgggguccggugcggagugcccuucguccuggga
aacggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgc
acguucguggggaaccuggcgcuaaaccauucguagacgaccugcuucug
ggucgggguuucguacguagcagagcagcucccucgcugcgaucuauuga
aagucagcccucgacacaaggguuugu

........................<<<<<<...............>>>>>
.>.........<<....>>..<<<<<<.....<<.....>>....>>>>>
>..<<<..<<<<<...<<<<<<<<<<.>>>>>>.>>>>.....>>>>>..
<<<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....<<<<.....
.>>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>
>>>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....
<<<<<<.>>>>>>..>>>................................
..<<....>>...............<<<<....>>>>.............
...................<<<<<<<<.<<<<.<<...<<<<<<<<.<<<
.....<<<<<<<<<<..>>>>>>>>>>......>>>.>>>.>>>>>...<
<<<<<<.<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<......<<<<
<<..>>>>>>.......>>>>>>.>>>........>>>>>>..>>>>>>>
>>>>..........<<<<<<.<..>.<<<<<<.>>>>.>>>>>>>>....
..>>.>>>>>...>>>>>..>>>>>>>>>..<<<<.<....>.>>>><<<
<<<....<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>
>>....<<<<<...<<<..<<<..>>>..>>>....>>>>>.<<<<<<<<
<.<<..>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<...<<<<<<
...>>>>>>......>.>>..<<<<<<......<<<.>>>..<<.<<<<<
<<...<<<.<<<<<<<<...>>>>>>...<<<<<<<<..>>>>>>>>...
.>>>>>>>>>>>>..>>..<<<<.<<<<<.....>>>>>.>>>>....<<
<......>>>...<<<<<<<...<<<(((.......<<<<<.....<<..
........<<<.<<<<<<<<<<.....<.<<<<<.<<<...<<.......
..>>...>>>.........<<......>>...>>>>>.>.>>>>>>>>>>
>>>..........))).>>...>>>>>..>>>...>>>>>>><<<<<<.<
<<...........>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<....
..<<<<.<<<<....>>>>>>>>...>>>>>>>>>>..>.....>>>>>>
<<.....<<.<<<<<<.......>>>>>>.<<<<....<<<<...<<<<.
..........>>>>..<<<<<...<<<<<<<....>>>>>>>......>>
.>>><<......>>.>>>><<<.....>>>..>>>>...<<<<<<.<<<<
<<<<..<<<<<<.>>>>>>.>>>.>>>>>>>>>>>......>>....>>.
..<<<<<<........>>>>>>....<<<<.<<<<......<<<<<<.<<
<<<<.<<<<<.<<<<<<<<<...<<<<<<<<<<.<<<<..........<<
<<<..<<<.>>>............>>>>>.>>>>.>>.>>>>>>>>..>>
>>>>>>>..>>>>>...<<<<<<<..<<<.........>>>>>>>>>>..
......>>>>>.>.>>>>>>.............<<<<<<...<..>...>
>>>>>.......((...<<<<<<<<<<<..<.<.<<<<<......>>>>>
...>.>.<<<.....))..>>>.....>>>>>....>>>>>>..<<<<<<
<....>>>.>>>>>>>>.>>>>..<<<<<<.<..<<<..<.<<<<<....
.............>>>>>.><<<<....<<<<.<<.<<<<<<<....>>>
>>..>>.>>...>>>>...>>>><<<<<...<<<<<...........>>>
>>...>>>>>.>>>...>.>>>>>>.<<<<<<<.<<..<<<<....<<<.
.......<<<<<.<<<<>>>>.>>>>>.......>>>...<<<..<<<<.
...<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>......
........>>>>..>>>>>>>>><<<<<.<.............>....<<
.<<<<<<<.<<.....<<<<....<<<<<......>>>>>...>>>>...
.>>....>>>>.>>>.>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkw Principles of human pre-60 S biogenesis.
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): P2 K3 K5 K7 R9 F13 R19 K20 R21 R27 R28 A31 R33 H41 H45 A46 S48 R50 K107 N109 S112 T144 K146 Q147 V154 R157 F158
• Binding residue (residue number reindexed from 1): P1 K2 K4 K6 R8 F12 R18 K19 R20 R26 R27 A30 R32 H40 H44 A45 S47 R49 K89 N91 S94 T126 K128 Q129 V136 R139 F140

Gene Ontology

Molecular Function

• GO:0003723 RNA binding

Biological Process

• GO:0042273 ribosomal large subunit biogenesis

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8fkw, PDBe:8fkw, PDBj:8fkw
• PDBsum: 8fkw
• PubMed: 37410842
• UniProt: Q9Y3C1|NOP16_HUMAN Nucleolar protein 16 (Gene Name=NOP16)