8OJ7 | pdb_00008oj7

HSV-1 DNA polymerase-processivity factor complex in halted elongation state

External Resource: Annotation

Domain Annotation: SCOP2 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)
B	SCOP2B Superfamily	DNA clamp	8036426	3000780	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA clamp	8036424	3000780	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF11590	DNA polymerase catalytic subunit Pol (DNAPolymera_Pol)	DNA polymerase catalytic subunit Pol	-	Family
A	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family
B	PF02282	DNA polymerase processivity factor (UL42) (Herpes_UL42)	DNA polymerase processivity factor (UL42)	The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerisation and makes little contribution to the catalyt ...	The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerisation and makes little contribution to the catalytic activity of the polymerase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase catalytic subunit	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity 5'-3' exonuclease activity exonuclease activity	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA replication	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex
B	DNA polymerase processivity factor	DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process bidirectional double-stranded viral DNA replication DNA biosynthetic process	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex
C	DNA (53-MER)	-	-	-
D	DNA (67-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A	IPR006172	DNA-directed DNA polymerase, family B	Family
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A	IPR050240	DNA polymerase type-B	Family
A	IPR021639	DNA polymerase catalytic subunit Pol, C-terminal	Domain
A	IPR042087	DNA polymerase family B, thumb domain	Homologous Superfamily
A	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily
B	IPR046938	DNA clamp superfamily	Homologous Superfamily
B	IPR003202	DNA polymerase processivity factor (UL42)	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.