1SRQ | pdb_00001srq

Crystal Structure of the Rap1GAP catalytic domain

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1srqd_	Multi-domain proteins (alpha and beta)	Rap/Ran-GAP	Rap/Ran-GAP	Rap/Ran-GAP	Rap1 GTPase-activating protein 1, Rap1GAP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1srqc_	Multi-domain proteins (alpha and beta)	Rap/Ran-GAP	Rap/Ran-GAP	Rap/Ran-GAP	Rap1 GTPase-activating protein 1, Rap1GAP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1srqb_	Multi-domain proteins (alpha and beta)	Rap/Ran-GAP	Rap/Ran-GAP	Rap/Ran-GAP	Rap1 GTPase-activating protein 1, Rap1GAP	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1srqa_	Multi-domain proteins (alpha and beta)	Rap/Ran-GAP	Rap/Ran-GAP	Rap/Ran-GAP	Rap1 GTPase-activating protein 1, Rap1GAP	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)
C	SCOP2B Superfamily	Rap/Ran-GAP	8039746	3001969	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rap/Ran-GAP	8039746	3001969	SCOP2B (2022-06-29)
A	SCOP2 Family	Rap/Ran-GAP	8027367	4002979	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rap/Ran-GAP	8039746	3001969	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)
D	Vinculin	e1srqD2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (v294.1)
C	Transpeptidase	e1srqC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Transpeptidase	ECOD (v294.1)
C	Usp	e1srqC2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Usp	ECOD (v294.1)
B	Transpeptidase	e1srqB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: Transpeptidase	ECOD (v294.1)
B	Usp	e1srqB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Usp	ECOD (v294.1)
A	Rap-GAP_dimer	e1srqA1	A: a+b three layers	X: a+b domain in Rap/Ran-GAP (Pfam 02145)	H: a+b domain in Rap/Ran-GAP (Pfam 02145)	T: a+b domain in Rap/Ran-GAP (Pfam 02145)	F: Rap-GAP_dimer	ECOD (v294.1)
A	Rap_GAP	e1srqA2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Rap_GAP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	6.10.140.210	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
C	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
C	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)
B	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
B	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)
A	3.30.1120.160	Alpha Beta	2-Layer Sandwich	Arylsulfatase, C-terminal domain		CATH (4.3.0)
A	3.40.50.11210	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Rap/Ran-GAP	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF21022	Rap/Ran-GAP protein dimerization domain (Rap-GAP_dimer)	Rap/Ran-GAP protein dimerization domain	This entry represents an alpha+beta domain found in some Rap-GAP proteins. It mediates dimerization in Rap1GAP protein [1].	Domain
A, B, C, D	PF02145	Rap/ran-GAP (Rap_GAP)	Rap/ran-GAP		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	GTPase-activating protein 1	small GTPase binding protein binding binding enzyme binding GTPase 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 identical protein binding protein homodimerization activity small GTPase binding protein binding binding enzyme binding GTPase 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 identical protein binding protein homodimerization activity protein dimerization activity pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation response to stimulus immune response immune system process adaptive immune response localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity positive regulation of cell adhesion regulation of cell adhesion positive regulation of biological process positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion regulation of cell-cell adhesion positive regulation of cellular process regulation of localization positive regulation of cellular component organization regulation of cellular component organization cellular component organization positive regulation of endocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport thyroid gland development negative regulation of thyroid gland epithelial cell proliferation gland development thyroid gland epithelial cell proliferation regulation of multicellular organismal process epithelial cell proliferation negative regulation of cell population proliferation cell population proliferation endocrine system development animal organ development regulation of cell population proliferation regulation of thyroid gland epithelial cell proliferation regulation of epithelial cell proliferation negative regulation of multicellular organismal process negative regulation of epithelial cell proliferation response to glial cell derived neurotrophic factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus cellular response to glial cell derived neurotrophic factor response to growth factor cell projection organization plasma membrane bounded cell projection assembly microvillus organization cellular component biogenesis regulation of microvillus assembly negative regulation of plasma membrane bounded cell projection assembly cellular component assembly negative regulation of cell projection organization plasma membrane bounded cell projection organization negative regulation of cellular component organization regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of microvillus organization regulation of plasma membrane bounded cell projection assembly negative regulation of microvillus assembly microvillus assembly cell projection assembly regulation of plasma membrane bounded cell projection organization cellular response to stimulus signaling signal transduction cell communication cellular localization establishment of localization in cell regulation of signaling small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle early endosome endosome cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle vesicle Golgi membrane Golgi apparatus bounding membrane of organelle organelle membrane cell body neuronal cell body axon

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR003109	GoLoco motif	Conserved Site
A, B, C, D	IPR000331	Rap/Ran-GAP domain	Domain
A, B, C, D	IPR035974	Rap/Ran-GAP superfamily	Homologous Superfamily
A, B, C, D	IPR050989	Rap1/Ran GTPase-activating	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P47736	melanoma acute promyelocytic leukemia thyroid adenoma malignant pancreatic neoplasm thyroid gland carcinoma ovarian cancer Pick disease Thyroid Neoplasm astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma nephrolithiasis pancreatic ductal adenocarcinoma pilocytic astrocytoma melanoma acute promyelocytic leukemia thyroid adenoma malignant pancreatic neoplasm thyroid gland carcinoma ovarian cancer Pick disease Thyroid Neoplasm astrocytic tumor glioblastoma large cell medulloblastoma malignant glioma nephrolithiasis pancreatic ductal adenocarcinoma pilocytic astrocytoma thyroid cancer adrenal cortex carcinoma atypical teratoid rhabdoid tumor interstitial cystitis lung cancer medulloblastoma oligodendroglioma pancreatic neoplasm primitive neuroectodermal tumor aortic stenosis cutaneous melanoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant ependymoma

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.