Structure of PDB 8fkx Chain NI Binding Site BS01

Receptor Information

>8fkx Chain NI (length=612) Species: 9606 (Homo sapiens)

DGEFEIQLPTFPTSGGFQSMGLSYPVFKGIMKKGYKVPTPIQRKTIPVIL
DGKDVVAMARTGSGKTACFLLPMFERLKTHSAQTGARALILSPTRELALQ
TLKFTKELGKFTGLKTALILGGDRMEDQFAALHENPDIIIATPGRLVHVA
VEMSLKLQSVEYVVFDEADRLFEMGFAEQLQEIIARLPGGHQTVLFSATL
PKLLVEFARAGLTEPVLIRLDVDTKLNEQLKTSFFLVREDTKAAVLLHLL
HNVVRPQDQTVVFVATKHHAEYLTELLTTQRVSCAHIYSALDPTARKINL
AKFTLGKCSTLIVTDLAARGLDIPLLDNVINYSFPAKGKLFLHRVGRVAR
AGRSGTAYSLVAPDEIPYLLDLHLFLGRSLTLARPLKEPSGVAGVDGMLG
RVPQSVVDEEDSGLQSTLEASLELRGLARVADNAQQQYVRSRPAPSPESI
KRAKEMDLVGLGLHPLFSSRFEEEELQRLRLVDSIKNYRSRATIFEINAS
SRDLCSQVMRAKRQKDRKAIARFQQGQQGRQEQQEGPDQEFYIPYRPKAF
EQQAAGAVLDLMGDEAQNLTRGRQQLKWDRKKKRFKKIKTESGRYISSSY
KRDLYQKWKQKQ

Ligand information

>8fkx Chain L3 (length=2250)

gcgaccucagaucagacguggcgacccgcugaaagcauauuagucagcgg
aggagaagaaacuaaccaggauucccucaguaacggcgagugaacaggga
agagcccagcgccgaauccccgccccgggggcgcgggacauguggcguac
ggaagacccgcuccccggcgccgcucguggggggcccaaguccuucugau
cgaggcccagcccguggacggugugaggccgguagcggcccccggcgcgc
cgggcccgggucuucccggagucggguugcuugggaaugcagcccaaagc
gggugguccaucuaaggcuaaauaccggcacgagaccgauagucaacaag
uaccguaagggaaaguugaaaagaacuuugaagagagaguucaagagggc
gugaaaccguuaagaggaacgggugggguccgcgcaguccgcccggagga
uucaacccggcggcggccgccgccgggcgcauuuccaccgcggcggugcg
ccgcgaccggcuccgggacggcugggaaggcccggcggggaagguggcuc
gggcccgaguguuacagcccccccggcagcagcacucgccgaaucccggg
gccgagggagcgccgcgcucuccggccgggccaggccacggagcgcacgg
ggucggcggcgacgucggcuacccacccgacccgucuugaaacacggacc
aaggagucuaacacgugcgcgagucgggggcucgcacgaaagccgccgug
gcgcaaggugggaucccgaggcccgccgagggcgcaccaccggcccgucu
cgcccggggagguggagcacgagcgcacguguuaggacccgaaagauggu
gaacuaugccgguauaggggcgaaagacuaaccaucuaguagcugguucc
cuccgaaguuucccggauagcuggcgcucuccgcaguuuuauccgguggg
uaagaagcccggcucgagccgggcguggaaugcgagugccuagugggcca
cuuuugguaagcagaacuggcgcugcgggaugaaccgaacgccggguuaa
ggcgcccgaugccgacgcucaucagaccccagaaaagguguugguugaua
uagacagcaggacgguggccauggaagucggaauccgcuaaggagugugu
aacaacucaccugccgaaucaacuagcccugaaaauggauggcgcuggag
cgucgggcccauacccggccgucgccggcagucacgcuacgccgcgacga
guaggagggccgcugcggugagccuugaagccuagggcgcgggcccgggu
ggagccgccgcaggugcagaucuuggugguaguagcauucaaacgagaac
uuugaaggccgaggggcgauggccuccggcccucgcggagagugaaucuc
gcuggcaauguagguaagggaagucgggaauccgauucccacugucccua
ccuacuauccagcgaaaccacagccaagggaacgggcuuggcggaaucag
cggggagaagacccuguugagcuugacucuagucuggcacggugaagaga
caugagagguguagaauaagugggaggcggccgccggugaaauaccacua
cucugaucguuuuuuccagugccagguggggaguuauccuucugaccuuu
uggguuuuaagcaggaggugucagaaaaguuaccacagggauaacuggcu
uguggcggccaagcgcgacgucgcuuuuugaugaugucggcucuuccuau
cauugugaagcagaauucaccaagcguuggauuguucacccacuaauagg
gaacgugagcuggggaccgucgugagacagguuagucccuacugaugguu
guugccaugguaauccugcucaguacgagaggaaccgcagguucagacau
uugguggugcuuggcugaggagccaauggggcgaagcuaccaucuguggg
auuaugacugaacgccucuaagucagaaucccgcccaggcggaacgauaa
gcgccgcggagccucgguuggccucggauagccgguccccgggguccggu
gcggagugcccuucguccugggaaacggggcgcggccggagaggcggccg
cccccucgcccgucacgcaccgcacguucguggggaaccuggcgcuaaac
cauucguagacgaccugcuucugggucgggguuucguacguagcagagca
gcucccucgcugcgaucuauugaaagucagcccucgacacaaggguuugu

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

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8fkx Principles of human pre-60 S biogenesis.
• Resolution: 2.59 Å
• Binding residue (original residue number in PDB): E177 G203 R205 H229 D445 P448 Q518 N579 R583 D584 S587 I601 F604 K735 F739 I751 T753 E754 S755 R757 I759 Y763 K770
• Binding residue (residue number reindexed from 1): E96 G122 R124 H148 D364 P367 Q437 N498 R502 D503 S506 I520 F523 K581 F585 I588 T590 E591 S592 R594 I596 Y600 K607

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003714 transcription corepressor activity
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0004386 helicase activity
• GO:0005102 signaling receptor binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0030331 nuclear estrogen receptor binding

Biological Process

• GO:0006364 rRNA processing
• GO:0006396 RNA processing
• GO:0016070 RNA metabolic process
• GO:0030520 estrogen receptor signaling pathway
• GO:0045892 negative regulation of DNA-templated transcription

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005730 nucleolus
• GO:0005794 Golgi apparatus
• GO:0016020 membrane

External links

• PDB: RCSB:8fkx, PDBe:8fkx, PDBj:8fkx
• PDBsum: 8fkx
• PubMed: 37410842
• UniProt: Q8TDD1|DDX54_HUMAN ATP-dependent RNA helicase DDX54 (Gene Name=DDX54)