5KG4

Human DNA polymerase eta-DNA ternary complex: reaction first with 1 mM Mn2+ for 1800s then with 10 mM Mg2+ for 60s

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	Lesion bypass DNA polymerase (Y-family), little finger domain	8101833	3000579	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8101834	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8101834	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ta1206-like	8101835	3001431	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	KOG2095_1st	e5kg4A2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: KOG2095_1st	ECOD (1.6)
A	IMS_C	e5kg4A4	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)
A	IMS	e5kg4A1	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)
A	IMS_1	e5kg4A3	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)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
A	3.40.1170.60	Alpha Beta	3-Layer(aba) Sandwich	MutS, DNA mismatch repair protein, domain I		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
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
A	PF00817	impB/mucB/samB family (IMS)	impB/mucB/samB family	-	Family
A	PF21704	DNApol eta/Rev1, HhH motif (POLH-Rev1_HhH)	DNApol eta/Rev1, HhH motif	-	Motif
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
B [auth T]	DNA (5'-D(CPAPTPTPAPTPGPAPCPGPCPT)-3')	-	-	-
C [auth P]	DNA (5'-D(APGPCPGPTPCPAPTP*A)-3')	-	-	-
A	DNA polymerase eta	DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid 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 DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid 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 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 postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair 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 postreplication repair response to stimulus nucleobase-containing compound biosynthetic process DNA synthesis involved in DNA repair macromolecule biosynthetic process error-free translesion synthesis nucleic acid biosynthetic process cellular response to stress biosynthetic process DNA damage response response to stress DNA biosynthetic process DNA repair response to radiation response to abiotic stimulus pyrimidine dimer repair response to light stimulus cellular response to radiation response to UV cellular response to environmental stimulus cellular response to UV-C response to UV-C cellular response to light stimulus cellular response to abiotic stimulus cellular response to UV error-prone translesion synthesis regulation of cellular process regulation of cellular response to stress regulation of primary metabolic process regulation of response to stress regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation regulation of macromolecule metabolic process regulation of DNA repair regulation of response to stimulus regulation of metabolic process regulation of DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle replication fork intracellular membraneless organelle chromosome site of double-strand break site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR052230	DNA polymerase eta	Family
A	IPR017961	DNA polymerase, Y-family, little finger domain	Domain
A	IPR041298	DNA polymerase eta, ubiquitin-binding zinc finger	Domain
A	IPR001126	UmuC domain	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR036775	DNA polymerase, Y-family, little finger domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y253	xeroderma pigmentosum xeroderma pigmentosum variant type acute myeloid leukemia Malignant neoplasm of breast tuberculosis breast cancer medulloblastoma malignant glioma 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.