2Q40 | pdb_00002q40

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	KOG4584	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: KOG4584	ECOD (1.6)
A	DUF89_C	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: DUF89_C	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 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 hydrolase activity catalytic activity cation binding metal ion binding	nucleoside phosphate metabolic process coenzyme A biosynthetic process amide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process coenzyme A biosynthetic process amide biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process amide metabolic process phosphorus metabolic process coenzyme A metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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 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.