2Q40

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At2g17340

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)
A	d2q40a_	Multi-domain proteins (alpha and beta)	AF1104-like	AF1104-like	AF1104-like	Hypothetical protein At2g17340	thale cress (Arabidopsis thaliana ) [TaxId: 3702 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	AF1104-like	8041849	3001930	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	F_UNCLASSIFIED	e2q40A1	A: alpha bundles	X: alpha-helical domain in AF1104-like proteins (From Topology)	H: alpha-helical domain in AF1104-like proteins (From Topology)	T: alpha-helical domain in AF1104-like proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF01937	e2q40A2	A: a/b three-layered sandwiches	X: Rossmann-like domain in AF1104-like proteins (From Topology)	H: Rossmann-like domain in AF1104-like proteins (From Topology)	T: Rossmann-like domain in AF1104-like proteins	F: PF01937	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1700.10	Mainly Alpha	Up-down Bundle	AF1104-like	AF1104-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01937	Damage-control phosphatase ARMT1-like domain (ARMT1-like_dom)	Damage-control phosphatase ARMT1-like domain	This domain is widely distributed in all domains of life and occur in stand-alone form and as C-terminal fusions to pantothenate kinase (PanK) in plants and animals. They are metal-dependent phosphatases involved in metabolic damage-control processes ...	This domain is widely distributed in all domains of life and occur in stand-alone form and as C-terminal fusions to pantothenate kinase (PanK) in plants and animals. They are metal-dependent phosphatases involved in metabolic damage-control processes termed "damage pre-emption" or "housecleaning". S.cerevisiae Damage-control phosphatase YMR027W and the human orthologue Damage-control phosphatase ARMT1 (also known as C6orf211) are involved in response to DNA damage, a damage pre-emption function. Crystal structure of Damage-control phosphatase At2g17340 from Arabidopsis revealed a novel protein fold and several conserved residues coordinating a metal ion (probably Mg2+), which exhibits a high degree of conservation, suggesting that the metal-binding site is central for the function [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein At2g17340	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity catalytic activity kinase activity transferase activity pantothenate kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups cation binding metal ion binding	ribose phosphate metabolic process nucleoside bisphosphate metabolic process coenzyme A biosynthetic process ribonucleoside bisphosphate biosynthetic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process ribose phosphate metabolic process nucleoside bisphosphate metabolic process coenzyme A biosynthetic process ribonucleoside bisphosphate biosynthetic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process organic substance metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process purine nucleoside bisphosphate biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process coenzyme A metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process cellular metabolic process nucleoside bisphosphate biosynthetic process primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process organic cyclic compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process purine nucleotide biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002791	Damage-control phosphatase ARMT1-like, metal-binding domain	Domain
A	IPR035073	At2g17340, three-helix bundle domain	Homologous Superfamily
A	IPR036075	Damage-control phosphatase ARMT1-like, metal-binding domain superfamily	Homologous Superfamily
A	IPR004567	Type II pantothenate kinase	Family
A	IPR016949	Damage-control phosphatase At2g17340	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.