Structure of PDB 8fkr Chain SW Binding Site BS01

Receptor Information

>8fkr Chain SW (length=445) Species: 9606 (Homo sapiens)

AFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAA
AKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLK
ELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGF
MYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE
DLARISLKKEPLYVGVDDDKANATVDGLEQGYVVCPSEKRFLLLFTFLKK
NRKKKLMVFFSSCMSVKYHYELLNYIDLPVLAIHGKQKQNKRTTTFFQFC
NADSGTLLCTDVAARGLDIPEVDWIVQYDPPDDPKEYIHRVGRTRGHALL
ILRPEELGFLRYLKQSKVPLSEFDFSWSKISDIQSQLEKLIEKNYFLHKS
AQEAYKSYIRAYDSHSLKQIFNVNNLNLPQVALSFGFKVPPFVDL

Ligand information

>8fkr Chain L3 (length=1767)

gcgaccucagaucagacguggcgacccgcugagcauauuagucagcggag
gagaagaaacuaaccaggauucccucaguaacggcgagugaacagggaag
agcccagcgccgaauccccgccccgggggcgcgggacauguggcguacgg
aagacccgcuccccggcgccgcucguggggggcccaaguccuucugaucg
aggcccagcccguggacggugugaggccgguagcggcccccggcgcgccg
ggcccgggucuucccggagucggguugcuugggaaugcagcccaaagcgg
gugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaagua
ccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggcgu
gaaaccguuaagaggacgggugggguccgcgcaguccgcccggaggauuc
aacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcgccg
cgaccggcuccgggacggcugggaaggcccggcggggaagguggcucggg
cccgaguguuacagcccccccggcagcagcacucgccgaaucccggggcc
gagcggcgacgucggcuacccacccgacccgucuacacggaccaaggagu
cuaacacgugcgcgagucgggggcucgcacgaaagccgccguggcgcaag
gugggaucccgaggccaguccgccgagggcgcaccaccggcccgucucgc
ccggggagguggagcacgagcgcacguguuaggacccgaagcugguuccc
uccgaaguuucccucaggauagcuggcgcucucgcaguuuuauccggggu
aagaagcccggcucgagccgggcguggaaugcgagugccuagugggccac
uuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaag
gcgcccgaugccgacgcucacccagaaaagguguugguugauauagacag
caggacgguggccauggaagucggaauccgcuaaggaguguguaacaacu
caccugccgaaucaacuagcccugaaaauggauggcgcuggagcgucggg
cccauacccggccgucgccggcagucgagaguggacggcgcggacgcuac
gccgcgacgaguaggagggccgcugcggugagccuugaagccuagggcgc
gggcccggguggagccgccgcaggugcagaucuuggugguaguagcaaug
uuggaacaauguaggaccuacuauccagcgaaaccagccaagcuuggcuc
agccuggcuuguggcggccaagcgcgacgucgcuuuuugugugaagcaga
auucaccaaacugaugauguguuguugccaugguaauccugcucaguacg
agaggaaccgcagguucagacauuugguguaugugcuuggcugaggagcc
aauggggcgaagcuaccaucugugggauuaugacugaacgccucuaaguc
agaaucccgcccaggcggaacgauagcgccgcggagccucgguuggccuc
ggauagccgguccccgggguccggugcggagugcccuucguccugggaaa
cggggcgcggccggagaggcggccgcccccucgcccgucacgcaccgcac
guucguggggaaccuggcgcuaaaccauucguagacgaccugcugggucg
ggguuucguacguagcagagcagcucccucgcugcgaucuauugaaagag
cccucgacacgguuugu

........................<<<<<<.............>>>>>.>
.........<<....>>..<<<<<<.....<<.....>>....>>>>>>.
.<<<..<<<<<...<<<<<<<<<<.>>>>>>.>>>>.....>>>>>..<<
<<<<<<<<...<<<<<<<<.<<.....<<<<<<<<....<<<<......>
>>>.....((......<<<.....))>>>...>.>>>>>>>.>>>>>>>>
>>..>>>>>>>>>>.......<<<<<<<........>>>>>>>.....<<
<<<<.>>>>>>..>>>..................................
<<....>>...............<<<<....>>>>...............
................<<<<<<<<..<<<......<<<<<<<<.<<<...
..<<<<<<<<<<..>>>>>>>>>>......>>>.>>>.>>>>>..<<<<<
<...<<<<<<<<<<<<<<<...<<..<<<.<<.<<<<......<<<<<<.
.>>>>>>.......>>>>>>.>>>........>>>>>>..>>>>>>>>>>
>.>>>>>>....>>>...>>>>>>>>..<<<<....>>>><<<<<<....
<<<<<<<<<<<<<..<<<...<<<<........>>>>.....>>>....<
<<<<...<<<..<<........>>..>>>....>>>>>.<<<<<<<<<.<
<..>>>>>>>>>.>>....>>>>>>>>>>>>>..<<.<...>.>>..<<<
<<<......<<<....>>>..<<.<<<<<<<..<<<.<<<<<<<<.>>>>
>>...<<<<<<<<..>>>>>>>>....>>>>>>>>>>>>..>>..<<<<.
<<<<<...[[>>>>>.>>>>....<<<......>>>...<<<<<<<...<
<<(((.......<<<<<....<<<....<<<.<<<<<<<<<<.......<
<<<<.<<<...<<.........>>...>>>.........<<......>>.
..>>>>>...>>>>>>>>>>>>>.....>>>..)))......>>>>>..>
>>...>>>>>>><<<<<<.<<<..............<.>...........
>>>>>>>>>....>>>>>>.<.<<<<<<<<.<<......<<<<.<<<<..
..>>>>>>>>...>>>>>>>>>>..>.....>>>>>><<.....<.....
.<<<<.....<<<<<.>>>>>..>>>>.>....>>.<<<<<<>>>>>><<
<<.]].......<<<<<<...<..>...>>>>>>......<<<<<.....
.>>>>>....>>>>......<<<<<<.<..<<<..<.<<<<<........
.........>>>>>.><<<<....<<<<...<.<..<<<<<<....>>>>
>>....>...>>>>>...>>>><<<<<...<<<<<...........>>>>
>...>>>>>.>>>...>.>>>>>>.<<<<<<.<<..<<<<....<<<...
.....<<<<<.<<<<>>>>.>>>>>.......>>>...<<<..<<<<...
.<<<<.<<<<<<<......>>>>>>>>>>>...>>>>..>>>........
......>>>>..>>>>>>>>.<<<<<.<.............>....<<<<
<<<<<<.....<<<<.<..<<<<<......>>>>>..>>>>>....>>.>
>>>>.>>>..>>>>>..

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkr Principles of human pre-60 S biogenesis.
• Resolution: 2.89 Å
• Binding residue (original residue number in PDB): K297 Y573 K577
• Binding residue (residue number reindexed from 1): K125 Y395 K399

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity

Biological Process

• GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

Cellular Component

• GO:0005634 nucleus
• GO:0005694 chromosome
• GO:0005730 nucleolus
• GO:0016020 membrane

External links

• PDB: RCSB:8fkr, PDBe:8fkr, PDBj:8fkr
• PDBsum: 8fkr
• PubMed: 37410842
• UniProt: Q9NVP1|DDX18_HUMAN ATP-dependent RNA helicase DDX18 (Gene Name=DDX18)