1DML | pdb_00001dml

CRYSTAL STRUCTURE OF HERPES SIMPLEX UL42 BOUND TO THE C-TERMINUS OF HSV POL

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
A	d1dmla1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	UL42	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)
C	d1dmlc1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	UL42	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)
E	d1dmle1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	UL42	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)
G	d1dmlg1	Alpha and beta proteins (a+b)	DNA clamp	DNA clamp	DNA polymerase processivity factor	UL42	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	DNA polymerase processivity factor	8024045	4002066	SCOP2 (2022-06-29)
A	SCOP2 Family	DNA polymerase processivity factor	8024047	4002066	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA clamp	8036424	3000780	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DNA clamp	8036426	3000780	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8036426	3000780	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA clamp	8036424	3000780	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA clamp	8036426	3000780	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA clamp	8036424	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8036424	3000780	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA clamp	8036426	3000780	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)
A	Herpes_UL42_1	e1dmlA2	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: Herpes_UL42_1	ECOD (1.6)
A	Herpes_UL42	e1dmlA1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: Herpes_UL42	ECOD (1.6)
C	Herpes_UL42	e1dmlC1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: Herpes_UL42	ECOD (1.6)
E	Herpes_UL42	e1dmlE1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: Herpes_UL42	ECOD (1.6)
G	Herpes_UL42	e1dmlG1	A: a+b two layers	X: DNA clamp (From Topology)	H: DNA clamp (From Topology)	T: DNA clamp	F: Herpes_UL42	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
C	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
E	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)
G	3.70.10.10	Alpha Beta	Box	Proliferating Cell Nuclear Antigen		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF11590	DNA polymerase catalytic subunit Pol (DNAPolymera_Pol)	DNA polymerase catalytic subunit Pol	-	Family
A, C, E, G	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
B, D, F, H	DNA POLYMERASE	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	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 metabolic process cellular 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 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
A, C, E, G	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

InterPro: Protein Family Classification InterPro Database Homepage

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