3E0J | pdb_00003e0j

X-ray structure of the complex of regulatory subunits of human DNA polymerase delta

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Metallo-dependent phosphatases	8053383	3001067	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-dependent phosphatases	8053383	3001067	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-dependent phosphatases	8053383	3001067	SCOP2B (2022-06-29)
G	SCOP2 Family	DNA polymerase subunit-like	8045195	4004346	SCOP2 (2022-06-29)
G	SCOP2 Family	DNA polymerase alpha OB-fold domain-like	8053385	4007079	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Metallo-dependent phosphatases	8053383	3001067	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Nucleic acid-binding proteins	8053386	3000135	SCOP2 (2022-06-29)
B	SCOP2 Family	PolD3 N-terminal domain-like	8044993	4004241	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Winged helix DNA-binding domain	8054002	3000034	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8054002	3000034	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Winged helix DNA-binding domain	8054002	3000034	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Winged helix DNA-binding domain	8054002	3000034	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	SRP_SPB	e3e0jA3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: SRP_SPB	ECOD (v294.1)
A		e3e0jA2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (v294.1)
C	Peptidase_M49	e3e0jC5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
C	Brix	e3e0jC2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
E	Peptidase_M49	e3e0jE5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
E	Brix	e3e0jE2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
G	Peptidase_M49	e3e0jG5	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
G	Brix	e3e0jG2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
B	CDC27	e3e0jB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: CDC27	ECOD (v294.1)
D	IL7	e3e0jD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
F	IL7	e3e0jF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
H	IL7	e3e0jH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.50	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
A	2.40.50.430	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
C	3.60.21.50	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
C	2.40.50.430	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	3.60.21.50	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
E	2.40.50.430	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	3.60.21.50	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)
G	2.40.50.430	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
B	3.90.1030.20	Alpha Beta	Alpha-Beta Complex	50s Ribosomal Protein L17	Chain: A,	CATH (4.3.0)
D	3.90.1030.20	Alpha Beta	Alpha-Beta Complex	50s Ribosomal Protein L17	Chain: A,	CATH (4.3.0)
F	3.90.1030.20	Alpha Beta	Alpha-Beta Complex	50s Ribosomal Protein L17	Chain: A,	CATH (4.3.0)
H	3.90.1030.20	Alpha Beta	Alpha-Beta Complex	50s Ribosomal Protein L17	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF04042	DNA polymerase alpha/epsilon subunit B (DNA_pol_E_B)	DNA polymerase alpha/epsilon subunit B	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	DNA polymerase subunit delta-2	DNA binding binding nucleic acid 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 nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process DNA-templated DNA replication nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation DNA strand elongation involved in DNA replication translesion synthesis cellular response to stimulus response to stimulus DNA damage tolerance DNA synthesis involved in DNA replication cellular response to stress DNA damage response response to stress error-prone translesion synthesis DNA repair	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome nucleoplasm
B, D, F, H	DNA polymerase subunit delta-3	protein-macromolecule adaptor activity molecular adaptor activity	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA-templated DNA replication DNA strand elongation DNA replication DNA strand elongation involved in DNA replication translesion synthesis cellular response to stimulus response to stimulus DNA damage tolerance DNA synthesis involved in DNA replication cellular response to stress DNA damage response response to stress error-prone translesion synthesis mismatch repair DNA repair nucleotide-excision repair, DNA gap filling nucleotide-excision repair DNA synthesis involved in DNA repair response to light stimulus cellular response to environmental stimulus cellular response to light stimulus cellular response to radiation response to UV UV-damage excision repair response to radiation response to abiotic stimulus cellular response to abiotic stimulus cellular response to UV DNA synthesis involved in UV-damage excision repair	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex zeta DNA polymerase complex transferase complex DNA polymerase complex intracellular protein-containing complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex nuclear chromosome chromosome intracellular organelle lumen intracellular organelle cellular anatomical structure nuclear replisome membraneless organelle replication fork delta DNA polymerase complex protein-DNA complex nuclear replication fork intracellular membraneless organelle intracellular membrane-bounded organelle organelle lumen organelle nuclear lumen replisome cytoplasm nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR024826	DNA polymerase delta/II small subunit family	Family
A, C, E, G	IPR007185	DNA polymerase alpha/delta/epsilon, subunit B	Domain
A, C, E, G	IPR040663	DNA polymerase delta subunit, OB-fold domain	Domain
A, C, E, G	IPR041863	DNA polymerase delta subunit 2, C-terminal domain	Domain
B, D, F, H	IPR019038	DNA polymerase delta subunit 3	Family
B, D, F, H	IPR041913	DNA polymerase delta subunit 3 superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: P49005	carpal tunnel syndrome metabolic syndrome X Sjogren syndrome lung cancer oligodendroglioma malignant ependymoma ovarian cancer
B, D, F, H	Pharos: Q15054	colorectal cancer colorectal adenoma Colorectal Neoplasms malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma medulloblastoma colorectal carcinoma malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm

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.