Annotations: 4XRP

Structure of the Pnkp1/Rnl/Hen1 RNA repair complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	PNKP ligase-like	8045746	4004657	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8091701	3000798	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	FlaF_Ig-like	e4xrpF1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: FlaF_Ig-like	ECOD (v295.2)
C	FlaF_Ig-like	e4xrpC1	A: alpha arrays	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: FlaF_Ig-like	ECOD (v295.2)
E		e4xrpE1	A: alpha arrays	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F:	ECOD (v295.2)
B		e4xrpB1	A: alpha arrays	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F:	ECOD (v295.2)
D		e4xrpD1	A: alpha arrays	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F:	ECOD (v295.2)
A		e4xrpA1	A: alpha arrays	X: Bromodomain-like	H: HTH	T: Three-helical HTH	F:	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (utative)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
D	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.40.50.1000	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HAD superfamily/HAD-like	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Hen1	RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding small RNA 2'-O-ribose methyltransferase activity RNA methyltransferase activity O-methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding small RNA 2'-O-ribose methyltransferase activity RNA methyltransferase activity O-methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity catalytic activity RNA 2'-O-methyltransferase activity	RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation regulation of cellular process negative regulation of biological process RNA metabolic process primary metabolic process nucleic acid metabolic process macromolecule methylation nucleobase-containing compound metabolic process RNA modification methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation regulation of cellular process negative regulation of biological process RNA biosynthetic process nucleic acid biosynthetic process negative regulation of cellular process RNA processing negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process siRNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B, E	Rnl	-	-	-
A, D	Pnkp1	phosphoric ester hydrolase activity deoxynucleotide 3'-phosphatase activity hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR053890	Hen1-like, N-terminal domain	Domain
C, F	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
C, F	IPR026610	3'-RNA ribose 2'-O-methyltransferase, Hen1	Family
B, E	IPR032380	Polynucleotide kinase-phosphatase, ligase domain	Domain
A, D	IPR056782	Polynucleotide kinase, PNKP phosphatase domain	Domain
A, D	IPR044493	Polynucleotide kinase PNKP, C-terminal phosphatase domain	Domain
A, D	IPR036412	HAD-like superfamily	Homologous Superfamily
A, D	IPR023214	HAD superfamily	Homologous Superfamily
A, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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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.