Structure of PDB 8fky Chain SZ Binding Site BS01

Receptor Information

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

PKAKGKTRRQKFGYSVNRKRLNRNARRKAAPRIECSHIRHAWDHAKSVRQ
NLAEMGLAVDPNRAVPLRLVRKPYVLNDLEAEASLPEKKGNTLSRDLIDY
VRYMVENHGEDYKAMARDEKNYYQDTPKQIRSKINVYKRFYPAEWQDFLD
SLQKRKMEVE

Ligand information

>8fky Chain L3 (length=2585)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagagguaaacgggugggguccgcgcaguccgcccggag
gauucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggug
cgccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggc
ucgggcccgaguguuacagcccccccggcagcagcacucgccgaaucccg
gggccgagggagcgccgcgcucuccggccgggccaggccacggagcgcac
ggggucggcggcgacgucggcuacccacccgacccgucuugaaacacgga
ccaaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccg
uggcgcaaggugggaucccgaggcccgccgagggcgcaccaccggcccgu
cucgcccggggagguggagcacgagcgcacguguuaggacccgaaagaug
gugaacuaugcaagccagaggaaacucugguggguauaggggcgaaagac
uaaccaucuaguagcugguucccuccgaaguuucccggauagcuggcgcu
cucgcgcaguuuuauccgguggguaagaagcccggcucgagccgggcgug
gaaugcgagugccuagugggccacuuuugguaagcagaacuggcgcugcg
ggaugaaccgaacgccggguuaaggcgcccgaugccgacgcucaucagac
cccagaaaagguguugguugauauagacagcaggacgguggccauggaag
ucggaauccgcuaaggaguguguaacaacucaccugccgaaucaacuagc
ccugaaaauggauggcgcuggagcgucgggcccauacccggccgucgccg
gcagucacgcuacgccgcgacgaguaggagggccgcugcggugagccuug
aagccuagggcgcgggcccggguggagccgccgcaggugcagaucuuggu
gguaguagcuucaaacgagaacuuugaaggccgaaguggagaaggguucc
auguacaugggucagucgguccuagggacgggcgauggccuccggcccgc
cggggagucggguucagauccccgaauccggaguggcggagaugggcgcc
gcgaggcguccagugcgguaacgcgaccgaucccggagaagccggcggga
gccccggggagaguucucuuuucuuugugaagggcagggcgcccuggaau
ggguucgccccgagagaggggcccgugccuuggaaagcgucgcgguuccg
gcggcguccggugagcucucgcuggcaauccgggggagaggguguaaauc
ucgcgccgggccguacccuccaaggugaacagccucuggcaauguaggua
agggaagucgggaauccgauucccacugucccuaccuacuauccagcgaa
accacagccaagggaacgggcuuggcggaaucagcggggagaagacccug
uugagcuugacucuagucuggcacggugaagagacaugagagguguagaa
uaagugggaggcggccgccggugaaauaccacuacucugaucguuuuuuc
cagugccagguggggaguuauccuucugaccuuuuggguuuuaagcagga
ggugucagaaaaguuaccacagggauaacuggcuuguggcggccaagcgc
gacgucgcuuuuugaugaugucggcucuuccuaucauugugaagcagaau
ucaccaagcguuggauuguucacccacuaauagggaacgugagcugggga
ccgucgugagacagguuagucccuacugaugguuguugccaugguaaucc
ugcucaguacgagaggaaccgcagguucagacauuugguggugcuuggcu
gaggagccaauggggcgaagcuaccaucugugggauuaugacugaacgcc
ucuaagucagaaucccgcccaggcggaacgauacagcgccgcggagccuc
gguuggccucggauagccgguccccgggguccggugcggagugcccuucg
uccugggaaacggggcgcggccggagaggcggccgcccccucgcccguca
cgcaccgcacguucguggggaaccuggcgcuaaaccauucguagacgacc
ugcuucugggucgggguuucguacguagcagagcagcucccucgcugcga
ucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fky Principles of human pre-60 S biogenesis.
• Resolution: 2.67 Å
• Binding residue (original residue number in PDB): P2 K3 K5 K7 R9 F13 R19 K20 R21 R27 R28 A31 H45 A46 S48 K107 N109 S112 D114 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 H44 A45 S47 K89 N91 S94 D96 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:8fky, PDBe:8fky, PDBj:8fky
• PDBsum: 8fky
• PubMed: 37410842
• UniProt: Q9Y3C1|NOP16_HUMAN Nucleolar protein 16 (Gene Name=NOP16)