1YM9

Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form

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
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ym9a2	Alpha and beta proteins (a/b)	Rhodanese/Cell cycle control phosphatase	Rhodanese/Cell cycle control phosphatase	Cell cycle control phosphatase, catalytic domain	CDC25b	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1ym9a3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	Rhodanese/Cell cycle control phosphatase	8044356	3000320	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	Rhodanese	e1ym9A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: Rhodanese/Cell cycle control phosphatase	F: Rhodanese	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.250.10	Alpha Beta	3-Layer(aba) Sandwich	Oxidized Rhodanese	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00581	Rhodanese-like domain (Rhodanese)	Rhodanese-like domain	Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	M-phase inducer phosphatase 2	protein binding binding kinase binding enzyme binding protein kinase binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity protein tyrosine phosphatase activity	cellular process cell cycle mitotic cell cycle regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process sexual reproduction reproductive process organelle fission cellular process cell cycle mitotic cell cycle regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process positive regulation of cellular process sexual reproduction reproductive process organelle fission meiotic cell cycle multicellular organismal reproductive process female gamete generation meiotic cell cycle process gamete generation cellular component organization nuclear division organelle organization meiosis I meiosis I cell cycle process female meiosis I female meiotic nuclear division meiotic nuclear division cellular component organization or biogenesis cell cycle process regulation of cytokinesis positive regulation of cell division regulation of cell cycle process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cell division regulation of cell cycle protein phosphorylation organonitrogen compound metabolic process phosphorylation cellular metabolic process primary metabolic process organic substance metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of cell cycle phase transition regulation of reproductive process cell cycle phase transition G2/MI transition of meiotic cell cycle positive regulation of reproductive process cell cycle G2/M phase transition regulation of meiotic cell cycle positive regulation of meiotic cell cycle phase transition positive regulation of G2/MI transition of meiotic cell cycle regulation of meiotic cell cycle phase transition positive regulation of meiotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition meiotic cell cycle phase transition positive regulation of cell cycle phase transition regulation of G2/MI transition of meiotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle mitotic cell cycle process G2/M transition of mitotic cell cycle mitotic cell cycle phase transition positive regulation of mitotic cell cycle phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of mitotic cell cycle phase transition developmental process cellular developmental process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction oocyte development anatomical structure maturation cell differentiation anatomical structure development germ cell development oocyte maturation oocyte differentiation cell maturation	intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle centrosome microtubule organizing center cytoplasm cytosol intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle intracellular non-membrane-bounded organelle spindle pole cellular anatomical entity microtubule cytoskeleton non-membrane-bounded organelle centrosome microtubule organizing center cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001763	Rhodanese-like domain	Domain
A	IPR036873	Rhodanese-like domain superfamily	Homologous Superfamily
A	IPR000751	M-phase inducer phosphatase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P30305	adrenal cortex carcinoma Chemical and Drug Induced Liver Injury esophageal adenocarcinoma osteosarcoma psoriasis atopic eczema gastric carcinoma interstitial cystitis pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis breast cancer Crohn disease drug-induced liver injury malignant mesothelioma pancreatic intraductal papillary-mucinous neoplasm

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.