2PYJ | pdb_00002pyj

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

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)
H [auth B]	d2pyjb1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of phi29 DNA polymerase	(Salasvirus phi29 ) [TaxId: 10756 ],	SCOPe (2.08)
H [auth B]	d2pyjb2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	phi29 DNA polymerase	(Salasvirus phi29 ) [TaxId: 10756 ],	SCOPe (2.08)
G [auth A]	d2pyja1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of phi29 DNA polymerase	(Salasvirus phi29 ) [TaxId: 10756 ],	SCOPe (2.08)
G [auth A]	d2pyja2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	phi29 DNA polymerase	(Salasvirus phi29 ) [TaxId: 10756 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8036151	3001272	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Ribonuclease H-like	8036150	3000143	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8036151	3001272	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8036151	3001272	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Ribonuclease H-like	8036150	3000143	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8036151	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)
H [auth B]		e2pyjB1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
H [auth B]	RNase_P_Rpp14	e2pyjB2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
H [auth B]	CBAH	e2pyjB3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: CBAH	ECOD (develop294)
H [auth B]	Hexokinase_2	e2pyjB4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Hexokinase_2	ECOD (develop294)
G [auth A]		e2pyjA1	A: alpha bundles	X: EGF-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (develop294)
G [auth A]	RNase_P_Rpp14	e2pyjA2	A: alpha bundles	X: EGF-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (develop294)
G [auth A]	CBAH	e2pyjA3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: CBAH	ECOD (develop294)
G [auth A]	Hexokinase_2	e2pyjA4	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Hexokinase_2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth B]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
H [auth B]	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
H [auth B]	3.30.1770.10	Alpha Beta	2-Layer Sandwich	TPR 1 domain of DNA polymerase	TPR 1 domain of DNA polymerase	CATH (4.3.0)
H [auth B]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
H [auth B]	4.10.80.20	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	DNA polymerase	CATH (4.3.0)
H [auth B]	4.10.80.30	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	DNA polymerase	CATH (4.3.0)
G [auth A]	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
G [auth A]	3.90.1600.10	Alpha Beta	Alpha-Beta Complex	Palm domain of DNA polymerase	B family DNA polymerase, palm domain	CATH (4.3.0)
G [auth A]	3.30.1770.10	Alpha Beta	2-Layer Sandwich	TPR 1 domain of DNA polymerase	TPR 1 domain of DNA polymerase	CATH (4.3.0)
G [auth A]	1.10.287.690	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	B family DNA polymerase, finger domain	CATH (4.3.0)
G [auth A]	4.10.80.20	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	DNA polymerase	CATH (4.3.0)
G [auth A]	4.10.80.30	Few Secondary Structures	Irregular	Rhinovirus 14, subunit 4	DNA polymerase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B]	PF03175	DNA polymerase type B, organellar and viral (DNA_pol_B_2)	DNA polymerase type B, organellar and viral	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth A], H [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 hydrolase activity, acting on ester bonds nuclease activity hydrolase activity exonuclease activity DNA binding 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 hydrolase activity, acting on ester bonds nuclease activity hydrolase activity exonuclease activity DNA binding binding nucleic acid binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding nucleoside phosphate binding nucleotide binding cation binding ion binding metal ion binding	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 DNA biosynthetic process	-
B [auth Y], D [auth R], E [auth K]	5'-d(ACACGTAAGCAGTC)-3'	-	-	-
A [auth X], C [auth Q], F [auth J]	5'-d(GACTGCTTA(DOC)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR006172	DNA-directed DNA polymerase, family B	Family
G [auth A], H [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR014416	DNA-directed DNA polymerase, family B, phi29-like virus	Family
G [auth A], H [auth B]	IPR017964	DNA-directed DNA polymerase, family B, conserved site	Conserved Site
G [auth A], H [auth B]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR004868	DNA-directed DNA polymerase, family B, mitochondria/virus	Domain
G [auth A], H [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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.