6VNP | pdb_00006vnp

Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dT

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)
L [auth J]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
I [auth G]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	3000579	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ta1206-like	8055757	3001431	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035590	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035589	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)
L [auth J]	IMS_HHH	e6vnpJ1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
L [auth J]	IMS_C	e6vnpJ4	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)
L [auth J]	IMS	e6vnpJ2	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)
L [auth J]	IMS_1	e6vnpJ3	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)
I [auth G]	IMS_HHH	e6vnpG1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
I [auth G]	IMS_C	e6vnpG2	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)
I [auth G]	IMS	e6vnpG4	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)
I [auth G]	IMS_1	e6vnpG3	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 D]	IMS_HHH	e6vnpD4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
F [auth D]	IMS_C	e6vnpD3	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 D]	IMS	e6vnpD1	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 D]	IMS_1	e6vnpD2	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)
C [auth A]	IMS_HHH	e6vnpA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH	ECOD (1.6)
C [auth A]	IMS_C	e6vnpA3	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)
C [auth A]	IMS	e6vnpA2	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)
C [auth A]	IMS_1	e6vnpA4	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)
L [auth J]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
L [auth J]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (utative)
L [auth J]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
L [auth J]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
I [auth G]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
I [auth G]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (utative)
I [auth G]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
I [auth G]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
F [auth D]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
F [auth D]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (utative)
F [auth D]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
F [auth D]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)
C [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
C [auth A]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (utative)
C [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (utative)
C [auth A]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], F [auth D], I [auth G], L [auth J]	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
C [auth A], F [auth D], I [auth G], L [auth J]	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
C [auth A], F [auth D], I [auth G], L [auth J]	PF11798	IMS family HHH motif (IMS_HHH)	IMS family HHH motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth P], D [auth B], G [auth E], J [auth H]	DNA (5'-D(PGPGPGPGPGPAPAPGPGPAPTPTPCPT)-3')	-	-	-
C [auth A], F [auth D], I [auth G], L [auth J]	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 damaged DNA binding nucleic acid binding	translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress translesion synthesis cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleic acid metabolic process DNA synthesis involved in DNA replication nucleobase-containing compound metabolic process nucleic acid biosynthetic process DNA replication biosynthetic process cellular response to stress DNA damage response response to stress metabolic process cellular process error-prone translesion synthesis macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication	cellular anatomical structure intracellular anatomical structure cytoplasm
B [auth T], E [auth C], H [auth F], K [auth I]	DNA (5'-D(TPTPCPAPT(R5M)PGPAPAPTPCPCPTPTPCPCPCPCP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], F [auth D], I [auth G], L [auth J]	IPR001126	UmuC domain	Domain
C [auth A], F [auth D], I [auth G], L [auth J]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth A], F [auth D], I [auth G], L [auth J]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
C [auth A], F [auth D], I [auth G], L [auth J]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth A], F [auth D], I [auth G], L [auth J]	IPR050116	DNA polymerase type-Y	Family
C [auth A], F [auth D], I [auth G], L [auth J]	IPR022880	DNA polymerase IV	Family
C [auth A], F [auth D], I [auth G], L [auth J]	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
C [auth A], F [auth D], I [auth G], L [auth J]	IPR024728	DNA polymerase type-Y, HhH motif	Conserved Site

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.