Structure of PDB 8fkw Chain NI

Receptor sequence

>8fkwNI (length=647) Species: 9606 (Homo sapiens)

DGEFEIQRPLPTFPTSGGFQSMGLSYPVFKGIMKKGYKVPTPIQRKTIPV
ILDGKDVVAMARTGSGKTACFLLPMFERLKTHSAQTGARALILSPTRELA
LQTLKFTKELGKFTGLKTALILGGDRMEDQFAALHENPDIIIATPGRLVH
VAVEMSLKLQSVEYVVFDEADRLFEMGFAEQLQEIIARLPGGHQTVLFSA
TLPKLLVEFARAGLTEPVLIRLDVDTKLNEQLKTSFFLVREDTKAAVLLH
LLHNVVRPQDQTVVFVATKHHAEYLTELLTTQRVSCAHIYSALDPTARKI
NLAKFTLGKCSTLIVTDLAARGLDIPLLDNVINYSFPAKGKLFLHRVGRV
ARAGRSGTAYSLVAPDEIPYLLDLHLFLGRSLTLARPLKEPSGVAGVDGM
LGRVPQSVVDEEDSGLQSTLEASLELRGLARVADNAQQQYVRSRPAPSPE
SIKRAKEMDLVGLGLHPLFSSRFEEEELQRLRLVDSIKNYRSRATIFEIN
ASSRDLCSQVMRAKRQKDRKAIARFQQGQQGRQEQQEGPDQEFYIPYRPK
AFEQQAAGAVLDLMGDEAQNLTRGRQQLKWDRKKKRFKKIKTESGRYISS
SYKRDLYQKWKQKQKIDDRDSRPELKTKQQILKQRRRAQKLHFLQRG

3D structure

• PDB: 8fkw Principles of human pre-60 S biogenesis.
• Chain: NI
• Resolution: 2.5 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	NI	G203 R205 H229 D445 P448 K535 N579 R583 S587 R591 F604 K731 W732 F739 K749 K750 T753 E754 S755 I759 S762 Y763 R765 K770 K774 Q827 Q828 K831 R834 R835 Q843 R844	G124 R126 H150 D366 P369 K456 N500 R504 S508 R512 F525 K579 W580 F587 K588 K589 T592 E593 S594 I598 S601 Y602 R604 K609 K613 Q629 Q630 K633 R636 R637 Q645 R646
BS02	ADP	NI	Y116 T120 Q123 T142 G143 G145 K146 T147	Y37 T41 Q44 T63 G64 G66 K67 T68

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