4DK3 | pdb_00004dk3

Structure of Editosome protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4dk3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B	d4dk3b2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
A	d4dk3a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
A	d4dk3a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PHP	e4dk3D2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PHP	ECOD (develop294)
C	PK_Tyr_Ser-Thr	e4dk3C1	A: alpha bundles	X: Flavodoxin-like	H: SH3	T: SH3	F: PK_Tyr_Ser-Thr	ECOD (develop294)
B	ABC_tran	e4dk3B1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
A	PK_Tyr_Ser-Thr	e4dk3A1	A: alpha bundles	X: Flavodoxin-like	H: SH3	T: SH3	F: PK_Tyr_Ser-Thr	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A, B	single domain antibody VHH	VH	Lama glama (llama)	IGHV3S101, IGHV3S301, IGHJ4*01	V-DOMAIN VH	IG	(VH)	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, B	Heavy Chain	IGHV1	-	rna-editing complex protein mp81	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	RNA-editing complex protein MP81	protein binding binding alpha-catenin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA modification macromolecule modification mitochondrial RNA modification metabolic process cellular process mitochondrial RNA metabolic process macromolecule metabolic process RNA nucleotide insertion RNA nucleotide deletion	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle
A, B	single domain antibody VHH	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR013087	Zinc finger C2H2-type	Domain
C, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
C, D	IPR017085	RNA editing complex, structural subunit MP81	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.