4DWJ | pdb_00004dwj

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4dwja_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
B	d4dwjb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
C	d4dwjc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
D	d4dwjd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
E	d4dwje_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
F	d4dwjf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
G	d4dwjg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)
H	d4dwjh_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Staphylococcus aureus subsp. aureus Mu50 ) [TaxId: 158878 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	3002021	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058430	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	SAM_1	e4dwjA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: SAM_1	ECOD (v294.1)
B	Flav_NS3-hel_C	e4dwjB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
C	Flav_NS3-hel_C	e4dwjC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
D	Flav_NS3-hel_C	e4dwjD2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
E	Flav_NS3-hel_C	e4dwjE2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
F	Flav_NS3-hel_C	e4dwjF2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
G	Flav_NS3-hel_C	e4dwjG2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)
H	Flav_NS3-hel_C	e4dwjH2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Flav_NS3-hel_C	ECOD (v294.1)

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)

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 deoxynucleoside phosphate kinase activity, ATP as phosphate donor nucleobase-containing compound kinase activity dTMP kinase activity kinase activity transferase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups	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 cytosol

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.