4ZBP | pdb_00004zbp

Crystal structure of the AMPCPR-bound AtNUDT7

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	SCOP2B Superfamily	Nudix associated domain-like	8091072	3002483	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nudix	8091074	3000098	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix associated domain-like	8091072	3002483	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nudix	8091074	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix	8091074	3000098	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nudix associated domain-like	8091072	3002483	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	Fumble	e4zbpA1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Fumble	ECOD (v294.1)
B	T_Ag_DNA_bind	e4zbpB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: RNA polymerase I subunits A49/A34.5 dimerization domains	F: T_Ag_DNA_bind	ECOD (v294.1)
C	Fumble	e4zbpC1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: Fumble	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF00293	NUDIX domain (NUDIX)	NUDIX domain		Domain
A, B, C	PF18290	Nudix hydrolase domain (Nudix_hydro)	Nudix hydrolase domain	This domain is found just before the N-terminal region of nucleoside diphosphate-linked moiety (Nudix) hydrolases (Pfam:PF00293). Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates which are often toxic metabolic intermediates and si ...	This domain is found just before the N-terminal region of nucleoside diphosphate-linked moiety (Nudix) hydrolases (Pfam:PF00293). Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates which are often toxic metabolic intermediates and signalling molecules [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Nudix hydrolase 7	pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity NAD+ diphosphatase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NADH pyrophosphatase activity ADP-glucose pyrophosphatase activity ADP-sugar pyrophosphatase activity ADP-ribose diphosphatase activity nucleoside diphosphate phosphatase activity ADP-ribose pyrophosphatase activity NAD binding pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity NAD+ diphosphatase activity dinucleotide phosphatase activity hydrolase activity, acting on acid anhydrides catalytic activity NADH pyrophosphatase activity ADP-glucose pyrophosphatase activity ADP-sugar pyrophosphatase activity ADP-ribose diphosphatase activity nucleoside diphosphate phosphatase activity ADP-ribose pyrophosphatase activity NAD binding binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process response to decreased oxygen levels cellular response to stimulus response to stimulus cellular response to oxygen levels cellular response to hypoxia cellular response to decreased oxygen levels cellular response to chemical stimulus cellular response to stress response to hypoxia response to stress response to chemical response to oxygen levels response to abiotic stimulus cellular process biological process involved in interspecies interaction between organisms response to other organism defense response immune response defense response to symbiont response to external stimulus cell death response to biotic stimulus symbiont-induced defense-related programmed cell death defense response to other organism immune system process plant-type hypersensitive response innate immune response response to external biotic stimulus programmed cell death regulation of cellular process glucan biosynthetic process regulation of starch biosynthetic process regulation of glucan biosynthetic process regulation of polysaccharide metabolic process regulation of primary metabolic process polysaccharide metabolic process glucan metabolic process regulation of carbohydrate metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process polysaccharide biosynthetic process carbohydrate biosynthetic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process biosynthetic process regulation of starch metabolic process starch metabolic process regulation of polysaccharide biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process starch biosynthetic process regulation of metabolic process response to oxidative stress response to ozone response to oxygen-containing compound response to reactive oxygen species defense response to bacterium response to bacterium regulation of defense response positive regulation of response to biotic stimulus regulation of response to biotic stimulus regulation of response to external stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway positive regulation of response to external stimulus immune response-regulating signaling pathway positive regulation of immune response regulation of response to stress regulation of immune system process signal transduction positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of innate immune response regulation of innate immune response regulation of response to stimulus positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response macromolecule modification protein poly-ADP-ribosylation protein metabolic process post-translational protein modification protein modification process response to osmotic stress response to salt stress	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A, B, C	IPR003293	Nudix hydrolase 6-like	Family
A, B, C	IPR040618	Pre-nudix hydrolase domain	Domain
A, B, C	IPR000086	NUDIX hydrolase domain	Domain
A, B, C	IPR020084	NUDIX hydrolase, conserved site	Conserved Site

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.