6UR9 | pdb_00006ur9

DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template, dideoxy primer, 3'-amino-ddGTP (nGTP), and Ca2+

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	DNA_pol_A_2nd	e6ur9D1	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: DNA_pol_A_2nd	ECOD (1.6)
D	DNA_pol_A_1st	e6ur9D3	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: DNA_pol_A_1st	ECOD (1.6)
D	DNA_pol_A_3rd	e6ur9D4	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_A_3rd	ECOD (1.6)
D	DNA_pol_A_exo1_1	e6ur9D2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1_1	ECOD (1.6)
A	DNA_pol_A_2nd	e6ur9A3	A: alpha arrays	X: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	H: helical bundle in Bacillus stearothermophilus-like DNA polymerase I (From Topology)	T: helical bundle in Bacillus stearothermophilus-like DNA polymerase I	F: DNA_pol_A_2nd	ECOD (1.6)
A	DNA_pol_A_1st	e6ur9A4	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: DNA_pol_A_1st	ECOD (1.6)
A	DNA_pol_A_3rd	e6ur9A1	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_A_3rd	ECOD (1.6)
A	DNA_pol_A_exo1_1	e6ur9A2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: DNA_pol_A_exo1_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
D	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (utative)
D	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
A	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (utative)
A	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	DNA (5'-D(GPCPGPAPTPCPAPGP*(DOC))-3')	-	-	-
C, F	DNA (5'-D(CPAPCPGPCPTPGPAPTPCPGPCP*A)-3')	-	-	-
A, D	DNA polymerase I	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 hydrolase activity, acting on ester bonds nuclease activity 3'-5' exonuclease activity 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 hydrolase activity, acting on ester bonds nuclease activity 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	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A, D	IPR054690	DNA polymerase I, 3'-5' exonuclease domain	Domain
A, D	IPR002298	DNA polymerase A	Family
A, D	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A, D	IPR018320	DNA polymerase 1	Family
A, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D	IPR002562	3'-5' exonuclease 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.