1ZMX | pdb_00001zmx

Crystal structure of D. melanogaster deoxyribonucleoside kinase N64D mutant 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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1zmxa_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
B	d1zmxb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
C	d1zmxc_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
D	d1zmxd_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
E	d1zmxe_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
F	d1zmxf_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
G	d1zmxg_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	SCOPe (2.08)
H	d1zmxh_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	automated matches	fruit fly (Drosophila melanogaster ) [TaxId: 7227 ],	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	8056726	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	3002021	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8056726	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		e1zmxA1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
B		e1zmxB1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
C		e1zmxC1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
D		e1zmxD1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
E		e1zmxE1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
F		e1zmxF1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
G		e1zmxG1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	F:	ECOD (20:10:01)
H		e1zmxH1	A: HTH	X: HTH	H: winged helix domain	T: MATH_2	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	PF01712	Deoxynucleoside kinase (dNK)	Deoxynucleoside kinase	This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the prod ...	This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyse the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process.	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	Deoxynucleoside 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 kinase activity transferase activity catalytic activity transferase activity, transferring phosphorus-containing groups nucleobase-containing compound kinase activity deoxynucleoside kinase activity deoxycytidine kinase activity nucleoside kinase activity uridine kinase activity phosphotransferase activity, alcohol group as acceptor deoxyadenosine kinase activity thymidine kinase activity cytidine kinase activity deoxyguanosine kinase activity	nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleobase-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process DNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleic acid biosynthetic process macromolecule metabolic process DNA biosynthetic process carbohydrate derivative biosynthetic process glycosyl compound biosynthetic process small molecule biosynthetic process nucleoside salvage carbohydrate derivative metabolic process nucleoside biosynthetic process nucleoside metabolic process nucleobase-containing small molecule biosynthetic process metabolic compound salvage	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm 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	IPR002624	Deoxynucleoside kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050566	Deoxyribonucleoside Kinase	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR031314	Deoxynucleoside kinase domain	Domain
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.