7F4Y

Crystal structure of replisomal dimer of DNA polymerase from bacteriophage RB69 with DNA duplexes

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)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8033949	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8033947	3000143	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	43_2nd	e7f4yA1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: 43_2nd	ECOD (1.6)
A	43_1st	e7f4yA2	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: 43_1st	ECOD (1.6)
A	DNA_pol_B_1st	e7f4yA4	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: DNA_pol_B_1st	ECOD (1.6)
A	DNA_pol_B_exo1_3rd	e7f4yA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)
D [auth B]	43_2nd	e7f4yB1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: thumb domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: 43_2nd	ECOD (1.6)
D [auth B]	43_1st	e7f4yB4	A: alpha bundles	X: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	H: fingers domain in bacteriophage RB69-like DNA polymerase I (From Topology)	T: fingers domain in bacteriophage RB69-like DNA polymerase I	F: 43_1st	ECOD (1.6)
D [auth B]	DNA_pol_B_1st	e7f4yB2	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: DNA_pol_B_1st	ECOD (1.6)
D [auth B]	DNA_pol_B_exo1_3rd	e7f4yB3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_B_exo1_3rd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF03104	DNA polymerase family B, exonuclease domain (DNA_pol_B_exo1)	DNA polymerase family B, exonuclease domain	-	Family
A, D [auth B]	PF00136	DNA polymerase family B (DNA_pol_B)	DNA polymerase family B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth T], E [auth S]	DNA (5'-D(TPCPAPAPGPTPAPAPGPCPAPGPTPCPCPGPCPTP*C)-3')	-	-	-
A, D [auth B]	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 organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 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 organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	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	-
C [auth P], F [auth Q]	DNA (5'-D(GPAPGPCPGPGPAPCPTPGPCPTPTPAP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D [auth B]	IPR006134	DNA-directed DNA polymerase, family B, multifunctional domain	Domain
A, D [auth B]	IPR034749	DNA-directed DNA polymerase T4 type	Family
A, D [auth B]	IPR006172	DNA-directed DNA polymerase, family B	Family
A, D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D [auth B]	IPR006133	DNA-directed DNA polymerase, family B, exonuclease domain	Domain
A, D [auth B]	IPR050240	DNA polymerase type-B	Family
A, D [auth B]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
A, D [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D [auth B]	IPR023211	DNA polymerase, palm domain superfamily	Homologous Superfamily

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.