1DEK

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP

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
Protein Modification Annotation
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1deka_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxynucleoside monophosphate kinase	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
B	d1dekb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Nucleotide and nucleoside kinases	Deoxynucleoside monophosphate kinase	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Adenylate kinase-like	8058367	4004025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	P-loop nucleotide/nucleoside kinase-like	8058368	3002021	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058368	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	P-mevalo_kinase_1	e1dekA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: P-mevalo_kinase_1	ECOD (1.6)
B	P-mevalo_kinase_1	e1dekB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: P-mevalo_kinase_1	ECOD (1.6)

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)
A	1.10.238.70	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	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)
B	1.10.238.70	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21448	Deoxynucleotide monophosphate kinase (DNMK)	Deoxynucleotide monophosphate kinase	This entry includes Deoxynucleotide monophosphate kinases from phages which act on dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	DEOXYNUCLEOSIDE MONOPHOSPHATE 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 deoxynucleoside-phosphate kinase activity, ATP as phosphate donor phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR048444	Deoxynucleotide monophosphate kinase	Family
A, B	IPR023191	Deoxynucleotide monophosphate kinase, N-terminal	Homologous Superfamily
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	OCS	Parent Component: CYS RESID: AA0556 PSI-MOD : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	(deoxy)nucleoside-phosphate kinase M-CSA #637	The deoxynucleotide kinase from phage T4 is able to catalyse the phosphorylation of GMP, methyl-CMP and TMP to the corresponding nucleotide diphosphate using ATP as the phosphate donor. This process is of particular interest because of the diverse specificity of the enzyme: most species deoxynucleotide kinases are only able to phosphorylate one dNMP, but owing to the selective pressure on the phage to have as small a genome as possible to allow easier infection of the bacteria, a wider specificity has developed. The sequence of the enzyme displays no homology to any other kinases, but does include the triphosphate binding consensus sequence.	Defined by 3 residues: ASP:A-15ARG:A-68HIS:A-206 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.4.13 (PDB Primary Data) Search M-CSA Motif + EC 2.7.4.13

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.