5HRL | pdb_00005hrl

The crystal structure of AsfvPolX: 1nt-gap(P) DNA2: dGTP ternary complex.

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8103729	3000129	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Nucleotidyltransferase-like	8103729	3000129	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	DNA_pol_B_palm	e5hrlA1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
E [auth B]	DNA_pol_B_palm	e5hrlB1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
E [auth B]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
E [auth B]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth B]	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
A, E [auth B]	PF01909	Nucleotidyltransferase domain (NTP_transf_2)	Nucleotidyltransferase domain	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTa ...	Members of this family belong to a large family of nucleotidyltransferases [1]. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth B]	DNA polymerase beta-like protein	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 cation binding ion binding metal ion 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 cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	virion component
B [auth C], F	DNA (5'-D(CPGPTPTPCPTPAPTPGPTPGPTPAPCPTPCPAPC)-3')	-	-	-
C [auth D], G	DNA (5'-D(GPTPGPAPGPTPAPCP*A)-3')	-	-	-
D [auth E], H	DNA (5'-D(PAPTPAPGPAPAPCPG)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth B]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A, E [auth B]	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
A, E [auth B]	IPR002934	Polymerase, nucleotidyl transferase domain	Domain
A, E [auth B]	IPR019843	DNA polymerase family X, binding site	Binding Site
A, E [auth B]	IPR022312	DNA polymerase family X	Family
A, E [auth B]	IPR029398	DNA polymerase beta, thumb domain	Domain

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.