2B8T

Crystal structure of Thymidine Kinase from U.urealyticum in complex with thymidine

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2b8tb1	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
B	d2b8tb2	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
C	d2b8tc1	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
C	d2b8tc2	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
D	d2b8td1	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
D	d2b8td2	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
A	d2b8ta1	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)
A	d2b8ta2	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 parvum ) [TaxId: 134821 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
C	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)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2B (2022-06-29)
A	SCOP2 Family	Type II thymidine kinase-like	8056701	4003437	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8056703	3000068	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8056702	3002019	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	TK_N	e2b8tB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: TK_N	ECOD (1.6)
B	TK_C	e2b8tB1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: TK_C	ECOD (1.6)
C	TK_N	e2b8tC2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: TK_N	ECOD (1.6)
C	TK_C	e2b8tC1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: TK_C	ECOD (1.6)
D	TK_N	e2b8tD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: TK_N	ECOD (1.6)
D	TK_C	e2b8tD1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: TK_C	ECOD (1.6)
A	TK_N	e2b8tA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: TK_N	ECOD (1.6)
A	TK_C	e2b8tA1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: TK_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 nucleoside kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process phosphorylation cellular metabolic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process cellular biosynthetic process primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process macromolecule metabolic process DNA biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity

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 National Science Foundation (DBI-1832184), 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 R01GM133198.