3AUO

DNA polymerase X from Thermus thermophilus HB8 ternary complex with 1-nt gapped DNA and ddGTP

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	HHH_5	e3auoB7	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
B	HHH_8	e3auoB8	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
B	DNA_pol_B_palm	e3auoB6	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
B	PHP	e3auoB5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PHP	ECOD (1.6)
A	HHH_5	e3auoA7	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_5	ECOD (1.6)
A	HHH_8	e3auoA8	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
A	DNA_pol_B_palm	e3auoA6	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
A	PHP	e3auoA5	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PHP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
B	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
B	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)
A	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
A	3.20.20.140	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Metal-dependent hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02811	PHP domain (PHP)	PHP domain	-	Family
A, B	PF14716	Helix-hairpin-helix domain (HHH_8)	Helix-hairpin-helix domain	-	Domain
A, B	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
A, B	PF14520	Helix-hairpin-helix domain (HHH_5)	Helix-hairpin-helix domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DNA polymerase beta family (X family)	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 organic cyclic compound binding nucleic acid binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds 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 organic cyclic compound binding nucleic acid binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds hydrolase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair bacterial-type flagellum-dependent swarming motility cellular response to stimulus response to stimulus primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair bacterial-type flagellum-dependent swarming motility bacterial-type flagellum-dependent cell motility cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
C [auth D], D [auth E]	1-nt gapped DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004013	PHP domain	Domain
A, B	IPR050243	Probable phosphatase PHP	Family
A, B	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
A, B	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
A, B	IPR029398	DNA polymerase beta, thumb domain	Domain
A, B	IPR016195	Polymerase/histidinol phosphatase-like	Homologous Superfamily
A, B	IPR022311	DNA polymerase/3'-5' exonuclease PolX-like	Family
A, B	IPR047967	PolX, PHP domain	Domain
A, B	IPR002008	DNA polymerase family X, beta-like	Family
A, B	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A, B	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
A, B	IPR003141	Polymerase/histidinol phosphatase, N-terminal	Domain
A, B	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A, B	IPR002054	DNA-directed DNA polymerase X	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.