1T3N | pdb_00001t3n

Structure of the catalytic core of DNA polymerase Iota in complex with DNA and dTTP

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth B]	d1t3nb1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	DNA polymerase iota	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth B]	d1t3nb2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DNA polymerase iota	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1t3na1	Alpha and beta proteins (a+b)	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	Lesion bypass DNA polymerase (Y-family), little finger domain	DNA polymerase iota	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1t3na2	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), catalytic domain	DNA polymerase iota	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035704	3001272	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Ta1206-like	8055758	3001431	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035701	3000579	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035704	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Lesion bypass DNA polymerase (Y-family), little finger domain	8035701	3000579	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035704	3001272	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Ta1206-like	8055758	3001431	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8035704	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)
D [auth B]	IMS_HHH_1	e1t3nB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: IMS_HHH_1	ECOD (v294.1)
D [auth B]	OKR_DC_1_C	e1t3nB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: OKR_DC_1_C	ECOD (v294.1)
D [auth B]	RNase_P_Rpp14	e1t3nB3	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
D [auth B]	Pkinase	e1t3nB4	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Pkinase	ECOD (v294.1)
C [auth A]	IMS_HHH_1	e1t3nA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: IMS_HHH_1	ECOD (v294.1)
C [auth A]	IMS	e1t3nA4	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 (v294.1)
C [auth A]	IMS	e1t3nA6	A: a+b three layers	X: Hypothetical protein Ta1206-like	H: Hypothetical protein Ta1206-like	T: Hypothetical protein Ta1206-like	F: IMS	ECOD (v294.1)
C [auth A]	IMS_C	e1t3nA2	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Lesion bypass DNA polymerase (Y-family), little finger domain	T: Lesion bypass DNA polymerase (Y-family), little finger domain	F: IMS_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
D [auth B]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
D [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D [auth B]	3.30.1490.100	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C [auth A]	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
C [auth A]	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
C [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C [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
C [auth A], D [auth B]	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
C [auth A], D [auth B]	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
C [auth A], D [auth B]	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
C [auth A], D [auth B]	polymerase (DNA directed) iota	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 damaged DNA binding nucleic acid binding cation binding ion 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 damaged DNA binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process translesion synthesis cellular response to stimulus response to stimulus nucleobase-containing compound biosynthetic process DNA damage tolerance macromolecule biosynthetic process DNA synthesis involved in DNA replication nucleic acid biosynthetic process biosynthetic process cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA biosynthetic process DNA repair	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cytoplasm supramolecular complex ribonucleoprotein granule membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear ribonucleoprotein granule nuclear lumen
B [auth P]	Primer DNA strand	-	-	-
A [auth T]	Template DNA strand	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR001126	UmuC domain	Domain
C [auth A], D [auth B]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth A], D [auth B]	IPR025527	HUWE1/REV1, ubiquitin-binding motif	Conserved Site
C [auth A], D [auth B]	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
C [auth A], D [auth B]	IPR053848	DNA polymerase IV/DNA polymerase iota-like, thumb domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A], D [auth B]	Pharos: Q9UNA4	psoriasis allergic rhinitis glioblastoma malignant ependymoma ovarian cancer gastric cancer hepatocellular carcinoma malignant mesothelioma progressive supranuclear palsy gastric carcinoma invasive ductal breast carcinoma osteosarcoma

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.