3LD9 | pdb_00003ld9

Crystal structure of thymidylate kinase from Ehrlichia chaffeensis at 2.15A resolution

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	d3ld9d1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
D	d3ld9d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
C	d3ld9c1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
C	d3ld9c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
B	d3ld9b1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
B	d3ld9b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
A	d3ld9a1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)
A	d3ld9a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Ehrlichia chaffeensis str. Arkansas ) [TaxId: 205920 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058426	3002021	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058426	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058426	3002021	SCOP2B (2022-06-29)
A	SCOP2 Family	Deoxynucleoside kinase-like	8058425	4004030	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8058426	3002021	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)
D	RVP	e3ld9D1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
C	RVP	e3ld9C1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
B	RVP	e3ld9B1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)
A	Peptidase_C1	e3ld9A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: HTH	T: winged helix domain	F: Peptidase_C1	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)
C	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)
A	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	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	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	IPR039430	Thymidylate kinase-like domain	Domain
A, B, C, D	IPR018094	Thymidylate kinase	Family
A, B, C, D	IPR018095	Thymidylate 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.