3DMO | pdb_00003dmo

1.6 A crystal structure of cytidine deaminase from Burkholderia pseudomallei

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	SCOP2B Superfamily	Cytidine deaminase-like	8059093	3001838	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cytidine deaminase-like	8059093	3001838	SCOP2B (2022-06-29)
B	SCOP2 Family	Cytidine deaminase	8059092	4000870	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cytidine deaminase-like	8059093	3001838	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Cytidine deaminase-like	8059093	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)
D	RasGEF	e3dmoD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.1)
C	RasGEF	e3dmoC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.1)
B	RasGEF	e3dmoB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: RasGEF	ECOD (v294.1)
A	Phage_endo_I	e3dmoA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: Phage_endo_I	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytidine deaminase	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines cytidine deaminase activity hydrolase activity catalytic activity deaminase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds identical protein binding protein binding	pyrimidine-containing compound metabolic process metabolic process cellular process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process primary 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	IPR050202	Cytidine and Deoxycytidylate Deaminase	Family
A, B, C, D	IPR006262	Cytidine deaminase, homotetrameric	Family
A, B, C, D	IPR002125	Cytidine and deoxycytidylate deaminase domain	Domain
A, B, C, D	IPR016192	APOBEC/CMP deaminase, zinc-binding	Binding Site
A, B, C, D	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.