4DIE | pdb_00004die

Crystal structure of a cytidylate kinase CmK from Mycobacterium abscessus bound to cytidine-5'-monophosphate

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	d4died1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
D	d4died2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
C	d4diec1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
C	d4diec2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
B	d4dieb1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
B	d4dieb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
A	d4diea1	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	SCOPe (2.08)
A	d4diea2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacteroides abscessus ATCC 19977 ) [TaxId: 561007 ],	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	8058378	3002021	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058378	3002021	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058378	3002021	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	P-loop nucleotide/nucleoside kinase-like	8058378	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)
D	Acyl-CoA_dh_M	e4dieD2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
C	Acyl-CoA_dh_M	e4dieC2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
B	Acyl-CoA_dh_M	e4dieB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Acyl-CoA_dh_M	ECOD (v294.1)
A	I-set	e4dieA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: I-set	ECOD (v294.1)

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	PF02224	Cytidylate kinase (Cytidylate_kin)	Cytidylate kinase	Cytidylate kinase EC:2.7.4.14 catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytidylate 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 nucleoside monophosphate kinase activity kinase activity transferase activity CMP kinase activity catalytic activity phosphotransferase activity, phosphate group as acceptor transferase activity, transferring phosphorus-containing groups deoxynucleoside phosphate kinase activity, ATP as phosphate donor dCMP kinase activity	nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process primary metabolic process nucleotide metabolic process pyrimidine nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nucleobase-containing small molecule interconversion	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003136	Cytidylate kinase	Family
A, B, C, D	IPR011994	Cytidylate kinase domain	Domain
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.