4DS5 | pdb_00004ds5

Ternary complex of Bacillus DNA Polymerase I Large Fragment, DNA duplex, and rCTP in presence of Mg2+

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)
B [auth D]	d4ds5d1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
B [auth D]	d4ds5d2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
A	d4ds5a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	automated matches	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)
A	d4ds5a2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	DNA polymerase I	automated matches	(Geobacillus kaustophilus HTA426 ) [TaxId: 235909 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8042337	3001272	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8042336	3000143	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8042337	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8042337	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8042336	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8042337	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)
B [auth D]		e4ds5D2	A: Thioredoxin-like	X: Thioredoxin-like	H: Thioredoxin-like	T: Exop_C	F:	ECOD (20:10:01)
B [auth D]		e4ds5D4	A: Alpha helical domain of ribonucleotide reductases	X: Alpha helical domain of ribonucleotide reductases	H: Alpha helical domain of ribonucleotide reductases	T: A2M_BRD	F:	ECOD (20:10:01)
A		e4ds5A9	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Fer4_13	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth D]	PF22619	DNA polymerase I, ribonuclease H-like domain (DNA_polI_exo1)	DNA polymerase I, ribonuclease H-like domain	This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other related enzymes. It is one of the constituent domains of Klenow fragment.	Domain
A, B [auth D]	PF00476	DNA polymerase family A (DNA_pol_A)	DNA polymerase family A		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth C], F	DNA (5'-D(CPAPTPGPGPGPAPGPTPCPAPGP*G)-3')	-	-	-
C [auth B], E	DNA (5'-D(CPCPTPGPAPCPTPCP*C)-3')	-	-	-
A, B [auth D]	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 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 5'-3' exonuclease activity 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, B [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B [auth D]	IPR002421	5'-3' exonuclease	Domain
A, B [auth D]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B [auth D]	IPR020045	DNA polymerase I-like, H3TH domain	Domain
A, B [auth D]	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A, B [auth D]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, B [auth D]	IPR054690	DNA polymerase I, 3'-5' exonuclease domain	Domain
A, B [auth D]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A, B [auth D]	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A, B [auth D]	IPR002298	DNA polymerase A	Family
A, B [auth D]	IPR020046	5'-3' exonuclease, alpha-helical arch, N-terminal	Domain
A, B [auth D]	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A, B [auth D]	IPR018320	DNA polymerase 1	Family
A, B [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B [auth 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.