4IRD

Structure of Polymerase-DNA complex

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth F]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8041930	3000579	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8041930	3000579	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)
E [auth F]	IMS_HHH	e4irdF7	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
E [auth F]	IMS_C	e4irdF6	A: a+b two layers	X: Reverse ferredoxin	H: Lesion bypass DNA polymerase (Y-family), little finger domain (From Topology)	T: Lesion bypass DNA polymerase (Y-family), little finger domain	F: IMS_C	ECOD (1.6)
E [auth F]	IMS	e4irdF5	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: IMS	ECOD (1.6)
E [auth F]	IMS_1	e4irdF4	A: a+b three layers	X: Hypothetical protein Ta1206-like (From Topology)	H: Hypothetical protein Ta1206-like (From Topology)	T: Hypothetical protein Ta1206-like	F: IMS_1	ECOD (1.6)
F [auth A]	IMS_HHH	e4irdA7	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
F [auth A]	IMS_C	e4irdA6	A: a+b two layers	X: Reverse ferredoxin	H: Lesion bypass DNA polymerase (Y-family), little finger domain (From Topology)	T: Lesion bypass DNA polymerase (Y-family), little finger domain	F: IMS_C	ECOD (1.6)
F [auth A]	IMS	e4irdA5	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: IMS	ECOD (1.6)
F [auth A]	IMS_1	e4irdA4	A: a+b three layers	X: Hypothetical protein Ta1206-like (From Topology)	H: Hypothetical protein Ta1206-like (From Topology)	T: Hypothetical protein Ta1206-like	F: IMS_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth F]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
E [auth F]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
E [auth F]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
E [auth F]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
F [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
F [auth A]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
F [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F [auth A]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth F], F [auth A]	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
E [auth F], F [auth A]	PF21999	DNA polymerase-iota, thumb domain (IMS_HHH_1)	DNA polymerase-iota, thumb domain	This is the thumb domain found in DNA polymerase iota and related proteins. This domain makes contacts with the minor groove of DNA.	Domain
E [auth F], F [auth A]	PF11799	impB/mucB/samB family C-terminal domain (IMS_C)	impB/mucB/samB family C-terminal domain	These proteins are involved in UV protection (Swiss).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], C [auth B]	DNA (5'-D(TPCPTPTPGPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	-	-	-
D [auth C]	DNA (5'-D(CPTPAPGPGPGPTPCPCPTPAPGPGPAPCPCP*C)-3')	-	-	-
B [auth H]	DNA (5'-D(GPGPGPTPCPCPTPAPGPGPAPCPCPC)-3')	-	-	-
E [auth F], F [auth A]	DNA polymerase IV	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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding organic cyclic compound binding damaged DNA binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process translesion synthesis postreplication repair primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process translesion synthesis postreplication repair primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA repair error-free translesion synthesis DNA-templated DNA replication DNA replication SOS response	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth F], F [auth A]	IPR001126	UmuC domain	Domain
E [auth F], F [auth A]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
E [auth F], F [auth A]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
E [auth F], F [auth A]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
E [auth F], F [auth A]	IPR050116	DNA polymerase type-Y	Family
E [auth F], F [auth A]	IPR022880	DNA polymerase IV	Family
E [auth F], F [auth A]	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
E [auth F], F [auth A]	IPR053848	DNA polymerase IV/DNA polymerase iota-like, thumb 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.