2UZ3 | pdb_00002uz3

Crystal Structure of Thymidine Kinase with dTTP from U. urealyticum

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d2uz3d1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	Thymidine kinase, TK1, N-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
D	d2uz3d2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Type II thymidine kinase zinc finger	Thymidine kinase, TK1, C-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
C	d2uz3c1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	Thymidine kinase, TK1, N-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
C	d2uz3c2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Type II thymidine kinase zinc finger	Thymidine kinase, TK1, C-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
B	d2uz3b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	Thymidine kinase, TK1, N-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
B	d2uz3b2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Type II thymidine kinase zinc finger	Thymidine kinase, TK1, C-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
A	d2uz3a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Type II thymidine kinase	Thymidine kinase, TK1, N-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)
A	d2uz3a2	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	Type II thymidine kinase zinc finger	Thymidine kinase, TK1, C-terminal domain	(Ureaplasma urealyticum ) [TaxId: 2130 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	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	Metallothio	e2uz3D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Metallothio	ECOD (develop294)
D	Bac_DnaA	e2uz3D2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Bac_DnaA	ECOD (develop294)
C	Metallothio	e2uz3C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Metallothio	ECOD (develop294)
C	Bac_DnaA	e2uz3C2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Bac_DnaA	ECOD (develop294)
B	Metallothio	e2uz3B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Metallothio	ECOD (develop294)
B	Bac_DnaA	e2uz3B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Bac_DnaA	ECOD (develop294)
A	Metallothio	e2uz3A1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Metallothio	ECOD (develop294)
A	Bac_DnaA	e2uz3A2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: Bac_DnaA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
D	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.30.60.20	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00265	Thymidine kinase (TK)	Thymidine kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	THYMIDINE KINASE	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding transition metal ion binding zinc ion binding metal ion binding thymidine kinase activity nucleobase-containing compound kinase activity deoxynucleoside kinase activity kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	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 pyrimidine-containing compound metabolic process deoxyribonucleoside metabolic process 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 pyrimidine-containing compound metabolic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process thymidine metabolic process pyrimidine deoxyribonucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001267	Thymidine kinase	Family
A, B, C, D	IPR020633	Thymidine kinase, conserved site	Conserved Site
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.