Structure of PDB 8fkv Chain SM Binding Site BS02

Receptor Information

>8fkv Chain SM (length=453) Species: 9606 (Homo sapiens)

SATNYITRNKARKKLQLSLADFRRLCILKGIYPHEPKHKKKVNKGSTAAR
TFYLIKDIRFLLHEPIVNKFREYKVFVRKLRKAYGKSEWNTVERLKDNKP
NYKLDHIIKERYPTFIDALRDLDDALSMCFLFSTFPRTGKCHVQTIQLCR
RLTVEFMHYIIAARALRKVFLSIKGIYYQAEVLGQPIVWITPYAFSHDHP
TDVDYRVMATFTEFYTTLLGFVNFRLYQLLNLHYPPKLEGQGTYALDSES
CMEKLAALSASLARVVVSAQEEDRRKELEAQEKHKKLFEGLKFFLNREVP
REALAFIIRSFGGEVSWDKSLCIGATYDVTDSRITHQIVDRPGQQTSVIG
RCYVQPQWVFDSVNARLLLPVAEYFSGVQLPPHLSPFVTEKEGDYVPPEK
LKLLALQRGREKYLYQKIMFGKRRKIREANKLAEKRKAHDEAVRSEKKAK
KAR

Ligand information

>8fkv Chain L3 (length=2213)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcgccgggcgcauuuccaccgcggcggugcgccgcgac
cggcuccgggacggcugggaaggcccggcggggaagguggcucgggcccg
aguguuacagcccccccggcagcagcacucgccgaaucccggggccgguc
ggcggcgacgucggcuacccacccgacccgucuugaaacacggaccaagg
agucuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgc
aaggugggaucccgaggcccaguccgccgagggcgcaccaccggccgcac
gagcgcacguguuaggacccgaaagauggugaaaccaucuaguagcuggu
ucccuccgaaguuucccggauagcuggcgcucuccgcaguuuuauccggu
ggguaagaagccggcguggaaugcgagugccuagugggccacuuuuggua
agcagaacuggcgcugcgggaugaaccgaacgccggguuaaggcgcccga
ugccgacgcucaucagaccccagaaaagguguugguugauauagacagca
ggacgguggccauggaagucggaauccgcuaaggaguguguaacaacuca
ccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucgggcc
cauacccggccgucgccggcagucgagaguggacggccgcggacgcuacg
ccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgcg
ggcccggguggagccgccgcaggugcagaucuuggugguaguagcauuca
aacgagaacuuugaaggccgaaguggagaaggggcgauggccuccggccc
ucgcggagaugggcgccgcgaggcguccagugaaucucgcccgcagcagg
ucuccggugaacagccucuggcaauguagguaagggaagucgggaauccg
auucccacugucccuaccuacuauccagcgaaaccacagccaagggaacg
ggcuuggcggaaucagcggggagaagacccuguugagcuugacucuaguc
uggcacggugaagagacaugagagguguagaauaagugggaggcggccgc
cggugaaauaccacuacucugaucguuuuuuccagugccagguggggagu
uauccuucugaccuuuuggguuuuaagcaggaggugucagaaaaguuacc
acagggauaacuggcuuguggcggccaagcgcgacgucgcuuuuugauga
ugucggcucuuccuaucauugugaagcagaauucaccaagcguuggauug
uucacccacuaauagggaacgugagcuggggaccgucgugagacagguuc
ccuacugaugguuguugccaugguaauccugcucaguacgagaggaaccg
cagguucagacauuugguggugcuuggcugaggagccaauggggcgaagc
uaccaucugugggauuaugacugaacgccucuaagucagaaucccgccca
ggcggaacgauaagcgccgcggagccucgguuggccucggauagccgguc
cccgggguccggugcggagugcccuucguccugggaaacggggcgcggcc
ggagaggcggccgcccccucgcccgucacgcaccgcacguucguggggaa
ccuggcgcuaaaccauucguagacgaccugcuucugggucgggguuucgu
acguagcagagcagcucccucgcugcgaucuauugaaagucagcccucga
cacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkv Principles of human pre-60 S biogenesis.
• Resolution: 2.47 Å
• Binding residue (original residue number in PDB): T19 N21 L31 A32 R35 R36 R62 Y85 K86 K91 R93 K94 Y96 R106 R149 T150 G151 K152 H154 V155 D214 V215 D216 R218 T222 R543 R560
• Binding residue (residue number reindexed from 1): T7 N9 L19 A20 R23 R24 R50 Y73 K74 K79 R81 K82 Y84 R94 R137 T138 G139 K140 H142 V143 D202 V203 D204 R206 T210 R410 R427

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0043021 ribonucleoprotein complex binding

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• GO:0006364 rRNA processing
• GO:0008283 cell population proliferation
• GO:0042254 ribosome biogenesis
• GO:0042273 ribosomal large subunit biogenesis
• GO:0051726 regulation of cell cycle

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005694 chromosome
• GO:0005730 nucleolus
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0030687 preribosome, large subunit precursor
• GO:0070545 PeBoW complex

External links

• PDB: RCSB:8fkv, PDBe:8fkv, PDBj:8fkv
• PDBsum: 8fkv
• PubMed: 37410842
• UniProt: O00541|PESC_HUMAN Pescadillo homolog (Gene Name=PES1)