3TMK | pdb_00003tmk

CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION

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)
A	d3tmka_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d3tmkb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d3tmkc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d3tmkd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d3tmke_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d3tmkf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G	d3tmkg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H	d3tmkh_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Thymidylate kinase	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Deoxynucleoside kinase-like	8058415	4004030	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058416	3002021	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		e3tmkA1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
B		e3tmkB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
C		e3tmkC1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
D		e3tmkD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
E		e3tmkE1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
F		e3tmkF1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
G		e3tmkG1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
H		e3tmkH1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	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)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
F	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
G	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02223	Thymidylate kinase (Thymidylate_kin)	Thymidylate kinase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	THYMIDYLATE 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 nucleobase-containing compound kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor nucleoside diphosphate kinase activity transferase activity, transferring phosphorus-containing groups deoxynucleoside phosphate kinase activity, ATP as phosphate donor dUMP kinase activity dTMP kinase activity	pyrimidine deoxyribonucleotide metabolic process pyrimidine deoxyribonucleoside diphosphate metabolic process deoxyribose phosphate biosynthetic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process nucleoside diphosphate biosynthetic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyrimidine deoxyribonucleotide metabolic process pyrimidine deoxyribonucleoside diphosphate metabolic process deoxyribose phosphate biosynthetic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process nucleoside diphosphate biosynthetic process deoxyribonucleotide biosynthetic process pyrimidine deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process deoxyribonucleoside diphosphate biosynthetic process pyrimidine-containing compound metabolic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process dUDP metabolic process nucleoside diphosphate metabolic process biosynthetic process organophosphate metabolic process pyrimidine deoxyribonucleoside diphosphate biosynthetic process organophosphate biosynthetic process pyrimidine nucleoside diphosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process dUDP biosynthetic process pyrimidine nucleotide biosynthetic process dTDP metabolic process dTDP biosynthetic process pyrimidine deoxyribonucleoside triphosphate biosynthetic process dTTP biosynthetic process pyrimidine deoxyribonucleoside triphosphate metabolic process pyrimidine nucleoside triphosphate biosynthetic process pyrimidine nucleoside triphosphate metabolic process dTTP metabolic process nucleoside triphosphate biosynthetic process nucleoside triphosphate metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR039430	Thymidylate kinase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018094	Thymidylate kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018095	Thymidylate kinase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	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.