4P9D | pdb_00004p9d

Crystal structure of dCMP deaminase from the cyanophage S-TIM5 in complex with dTMP and dTTP.

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytidine deaminase-like	8077747	3001838	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)
F	Peptidase_S8	e4p9dF1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)
E	Peptidase_S8	e4p9dE1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)
D	Peptidase_S8	e4p9dD1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)
C	Peptidase_S8	e4p9dC1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)
B	Peptidase_S8	e4p9dB1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)
A	Peptidase_S8	e4p9dA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: PEBP-like	F: Peptidase_S8	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
E	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
D	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
C	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
B	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	CATH (4.3.0)
A	3.40.140.10	Alpha Beta	3-Layer(aba) Sandwich	Cytidine Deaminase	domain 2	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	PF00383	Cytidine and deoxycytidylate deaminase zinc-binding region (dCMP_cyt_deam_1)	Cytidine and deoxycytidylate deaminase zinc-binding region		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	Deoxycytidylate deaminase	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines hydrolase activity catalytic activity deaminase activity dCMP deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines hydrolase activity catalytic activity deaminase activity dCMP deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR016473	Deoxycytidylate deaminase	Family
A, B, C, D, E A, B, C, D, E, F	IPR015517	Deoxycytidylate deaminase-related	Family
A, B, C, D, E A, B, C, D, E, F	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A, B, C, D, E A, B, C, D, E, F	IPR016193	Cytidine deaminase-like	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.