3KVH

Crystal structure of human protein syndesmos (NUDT16-like protein)

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	d3kvha_	Alpha and beta proteins (a+b)	Nudix	Nudix	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nudix	8086556	3000098	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	NUDIX_3	e3kvhA1	A: a+b two layers	X: beta-Grasp	H: Nudix (From Topology)	T: Nudix	F: NUDIX_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.79.10	Alpha Beta	Alpha-Beta Complex	Nucleoside Triphosphate Pyrophosphohydrolase	Nucleoside Triphosphate Pyrophosphohydrolase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22327	U8 snoRNA-decapping enzyme-like (Nudt16-like)	U8 snoRNA-decapping enzyme-like	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later report ...	This entry represents the NUDIX hydrolase domain of U8 snoRNA -decapping enzyme from Xenopus laevis (Nudt16) and similar proteins from animals and bacteria. Nudt16 was initially described as an RNA-binding and decapping enzyme but it was later reported to be specialised in the removal of hazardous (deoxy)inosine diphosphate from the nucleotide pool. It adopts a canonical NUDIX fold, an alpha-beta-alpha sandwich constituted by two beta-sheets whose strands interact in a way that could also be described as a single extended beta-sheet [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein syndesmos	RNA binding binding organic cyclic compound binding snoRNA binding nucleic acid binding	cellular response to stimulus regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress negative regulation of biological process negative regulation of double-strand break repair via nonhomologous end joining regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of DNA repair cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process cellular response to stimulus regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress negative regulation of biological process negative regulation of double-strand break repair via nonhomologous end joining regulation of primary metabolic process nucleobase-containing compound metabolic process negative regulation of DNA repair cellular response to stress response to stress regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of double-strand break repair via nonhomologous end joining DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process double-strand break repair via nonhomologous end joining negative regulation of response to stimulus negative regulation of metabolic process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus metabolic process cellular process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR015797	NUDIX hydrolase-like domain superfamily	Homologous Superfamily
A	IPR051894	Nudix_hydrolase_NUDT16_sf	Unknown

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.