5FJ7 | pdb_00005fj7

Structure of the P2 polymerase inside in vitro assembled bacteriophage phi6 polymerase complex, with P1 included

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033169	3001272	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	RdRP_1_C	e5fj7C2	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: RdRP_1_C	ECOD (1.6)
C	RdRP_1_N	e5fj7C1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RdRP_1_N	ECOD (1.6)
B	EUF08573	e5fj7B1	A: a+b complex topology	X: Major inner capsid protein P1 (From Topology)	H: Major inner capsid protein P1 (From Topology)	T: Major inner capsid protein P1	F: EUF08573	ECOD (1.6)
A	EUF08573	e5fj7A1	A: a+b complex topology	X: Major inner capsid protein P1 (From Topology)	H: Major inner capsid protein P1 (From Topology)	T: Major inner capsid protein P1	F: EUF08573	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00680	Viral RNA-dependent RNA polymerase (RdRP_1)	Viral RNA-dependent RNA polymerase	-	Family
A, B	PF20837	Major inner capsid protein P1 (P1)	Major inner capsid protein P1	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	RNA-DIRECTED RNA POLYMERASE	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding uridylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity RNA uridylyltransferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA-directed RNA polymerase activity binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding uridylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity RNA uridylyltransferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase activity RNA binding nucleic acid binding cation binding ion binding metal ion binding	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process gene expression DNA-templated transcription	virion component
A, B	MAJOR INNER PROTEIN P1	RNA binding binding nucleic acid binding identical protein binding protein binding	-	viral capsid icosahedral viral capsid virion component viral inner capsid viral nucleocapsid T=2 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR007096	RNA-directed RNA polymerase, catalytic domain, bacteriophage	Domain
C	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
C	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C	IPR043110	Cystovirus, RNA-directed RNA polymerase, N-terminal	Homologous Superfamily
C	IPR016406	Cystovirus, RNA-directed RNA polymerase	Family
A, B	IPR048856	Major inner capsid protein P1	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.