BioLiP

Structure of PDB 9fmd Chain W

Receptor sequence

>9fmdW (length=513) Species: 9606 (Homo sapiens) [Search protein sequence]

ETGVHLDPAVKEVQYNPTYETMFAPEFGPENPFRTQQMAAPRNMLSGYAE
PAHINDFMFEQQRRTFATYGYALDPSLDNHQVSAKYIGSVEEAEKNQGLT
VFETGQKKTEKRKKFKENDASNIDGFLGPWAKYVDEKDVAKPSEEEQKEL
DEITAKRQKKGKQEEEKPGEEKTILHVKEMYDYQGRSYLHIPQDVGVNLR
STMPPEKCYLPKKQIHVWSGHTKGVSAVRLFPLSGHLLLSCSMDCKIKLW
EVYGERRCLRTFIGHSKAVRDICFNTAGTQFLSAAYDRYLKLWDTETGQC
ISRFTNRKVPYCVKFNPDEDKQNLFVAGMSDKKIVQWDIRSGEIVQEYDR
HLGAVNTIVFVDENRRFVSTSDDKSLRVWEWDIPVDFKYIAEPSMHSMPA
VTLSPNGKWLACQSMDNQILIFGAQNRFRLNKKKIFKGHMVAGYACQVDF
SPDMSYVISGDGNGKLNIWDWKTTKLYSRFKAHDKVCIGAVWHPHETSKV
ITCGWDGLIKLWD

3D structure

PDB

9fmd Mechanism for the initiation of spliceosome disassembly.

Chain

Resolution

3.3 Å

3D
structure

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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	W	K273 Y275 L276 K454 R493 Y543 T563 D579	K207 Y209 L210 K388 R427 Y477 T497 D513
BS02	rna	W	R130 T134 V167 F168 T170 R223 L418	R64 T68 V101 F102 T104 R157 L352

Gene Ontology

	Molecular Function
GO:0003723	RNA binding
GO:0003729	mRNA binding
GO:0005515	protein binding

	Biological Process
GO:0000398	mRNA splicing, via spliceosome
GO:0006397	mRNA processing
GO:0008380	RNA splicing
GO:1990403	embryonic brain development

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005681	spliceosomal complex
GO:0016607	nuclear speck
GO:0071007	U2-type catalytic step 2 spliceosome
GO:0071013	catalytic step 2 spliceosome

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Molecular Function

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Biological Process

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Cellular Component

PDB	RCSB:9fmd, PDBe:9fmd, PDBj:9fmd
PDBsum	9fmd
PubMed	38925148
UniProt	O60508\|PRP17_HUMAN Pre-mRNA-processing factor 17 (Gene Name=CDC40)