5MY3 | pdb_00005my3

Crystal structure of the RhoGAP domain of Rgd1p at 2.19 Angstroms resolution

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	d5my3a1	All alpha proteins	GTPase activation domain, GAP	GTPase activation domain, GAP	automated matches	automated matches	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d5my3a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	BCR-homology GTPase activation domain (RhoGAP-domain)	8079468	4001255	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GTPase activation domain, GAP	8079469	3001163	SCOP2 (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	Gal-bind_lectin	e5my3A1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: Gal-bind_lectin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.555.10	Mainly Alpha	Orthogonal Bundle	Phosphatidylinositol 3-kinase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00620	RhoGAP domain (RhoGAP)	RhoGAP domain	GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	RHO GTPase-activating protein RGD1	phosphatidylinositol-3,5-bisphosphate binding ion binding binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding small molecule binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity phosphatidylinositol-3,5-bisphosphate binding ion binding binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding small molecule binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity phosphatidylinositol-4,5-bisphosphate binding phosphatidylinositol-4-phosphate binding phosphatidylinositol-5-phosphate binding phosphatidylinositol-3-phosphate binding identical protein binding protein binding	establishment of cell polarity cellular process establishment or maintenance of cell polarity cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization response to stimulus response to pH response to abiotic stimulus response to acidic pH positive regulation of autophagy establishment of cell polarity cellular process establishment or maintenance of cell polarity cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization response to stimulus response to pH response to abiotic stimulus response to acidic pH positive regulation of autophagy regulation of biological process catabolic process regulation of cellular process autophagy biological regulation positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process metabolic process process utilizing autophagic mechanism regulation of metabolic process positive regulation of cellular process response to osmotic stress response to stress cellular response to stimulus small GTPase-mediated signal transduction signaling intracellular signal transduction cell communication intracellular signaling cassette signal transduction septin ring organization septin cytoskeleton organization	cellular anatomical structure cell tip cell pole cell cortex intracellular anatomical structure cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton cell periphery intracellular organelle endocytic patch cytoskeleton organelle membraneless organelle cellular anatomical structure cell tip cell pole cell cortex intracellular anatomical structure cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton cell periphery intracellular organelle endocytic patch cytoskeleton organelle membraneless organelle cortical actin cytoskeleton actin cortical patch cytoplasm cell projection mating projection mating projection tip plasma membrane bounded cell projection site of polarized growth cell division site plasma membrane membrane cellular bud ascospore-type prospore prospore membrane intracellular immature spore

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A	IPR050729	Rho GTPase-activating protein	Family
A	IPR031160	F-BAR domain	Domain
A	IPR000198	Rho GTPase-activating protein domain	Domain
A	IPR001060	FCH domain	Domain

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.