4DF4 | pdb_00004df4

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentinyl)-7-deaza-2 -dATP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4df4a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	DnaQ-like 3'-5' exonuclease	Exonuclease domain of prokaryotic DNA polymerase	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)
A	d4df4a2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	DNA polymerase I (Klenow fragment)	(Thermus aquaticus ) [TaxId: 271 ],	SCOPe (2.08)

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	8037492	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037492	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8044539	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		e4df4A1	A: P-loop domains-like	X: RIFT-related	H: FMN-binding split barrel 2	T: Ras	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.20.1060.10	Mainly Alpha	Up-down Bundle	Taq DNA Polymerase	Chain T, domain 4	CATH (4.3.0)
A	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA polymerase I, thermostable	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 binding heterocyclic compound binding carbohydrate derivative 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 binding heterocyclic compound binding carbohydrate derivative binding small molecule binding hydrolase activity, acting on ester bonds nuclease activity 5'-3' exonuclease activity hydrolase activity exonuclease activity	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	-
B	DNA (5'-D(GPAPCPCPAPCPGPGPCPGPCP(DOC))-3')	-	-	-
C	DNA (5'-D(APAPAPTPGPGPCPGPCPCPGPTPGPGPTPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR002421	5'-3' exonuclease	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR020045	DNA polymerase I-like, H3TH domain	Domain
A	IPR015361	Taq polymerase, thermostable, exonuclease region	Domain
A	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A	IPR002298	DNA polymerase A	Family
A	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
A	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A	IPR018320	DNA polymerase 1	Family
A	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A	IPR012337	Ribonuclease H-like 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.