3L43 | pdb_00003l43

Crystal structure of the dynamin 3 GTPase domain bound with GDP

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	d3l43d_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3l43c_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3l43b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3l43a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	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)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8054366	3002022	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)
D	Peptidase_S9, Abhydrolase_4, Hydrolase_4	e3l43D1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Peptidase_S9, Abhydrolase_4, Hydrolase_4	ECOD (v294.1)
C	Peptidase_S9, Abhydrolase_4, Hydrolase_4	e3l43C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Peptidase_S9, Abhydrolase_4, Hydrolase_4	ECOD (v294.1)
B	Peptidase_S9, Abhydrolase_4, Hydrolase_4	e3l43B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Peptidase_S9, Abhydrolase_4, Hydrolase_4	ECOD (v294.1)
A	Peptidase_M42	e3l43A1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Peptidase_M42	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01031	Dynamin central region (Dynamin_M)	Dynamin central region	-	Family
A, B, C, D	PF00350	Dynamin family (Dynamin_N)	Dynamin family		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dynamin-3	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cytoskeletal protein binding microtubule binding protein binding tubulin binding 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 identical protein binding	localization import into cell transport cellular process endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization vesicle budding from membrane cellular localization synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse cellular component organization localization import into cell transport cellular process endocytosis establishment of localization vesicle-mediated transport establishment of organelle localization vesicle budding from membrane cellular localization synaptic vesicle cycle presynaptic endocytosis vesicle-mediated transport in synapse cellular component organization vesicle organization synaptic vesicle recycling organelle localization establishment of localization in cell synaptic vesicle budding cellular component organization or biogenesis synaptic vesicle localization synaptic vesicle endocytosis membrane organization vesicle localization establishment of vesicle localization synaptic vesicle budding from presynaptic endocytic zone membrane organelle organization synaptic vesicle transport cellular component biogenesis filopodium assembly cellular component assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cell projection assembly developmental process multicellular organismal process nervous system development multicellular organism development cell junction organization cell junction assembly anatomical structure development synapse organization synapse assembly system development	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane presynapse synapse extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane presynapse synapse cell junction intracellular anatomical structure cytoplasm neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse perinuclear region of cytoplasm polymeric cytoskeletal fiber intracellular membraneless organelle intracellular organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020850	GTPase effector domain	Domain
A, B, C, D	IPR001849	Pleckstrin homology domain	Domain
A, B, C, D	IPR001401	Dynamin, GTPase domain	Domain
A, B, C, D	IPR045063	Dynamin, N-terminal	Domain
A, B, C, D	IPR030381	Dynamin-type guanine nucleotide-binding (G) domain	Domain
A, B, C, D	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR019762	Dynamin, GTPase region, conserved site	Conserved Site
A, B, C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D	IPR003130	Dynamin GTPase effector	Domain
A, B, C, D	IPR000375	Dynamin stalk domain	Domain
A, B, C, D	IPR022812	Dynamin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9UQ16	osteosarcoma pilocytic astrocytoma progressive supranuclear palsy ulcerative colitis Alzheimer disease Crohn disease gastric carcinoma kidney neoplasm lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer subependymal giant cell astrocytoma uterine corpus leiomyoma osteosarcoma pilocytic astrocytoma progressive supranuclear palsy ulcerative colitis Alzheimer disease Crohn disease gastric carcinoma kidney neoplasm lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer subependymal giant cell astrocytoma uterine corpus leiomyoma astrocytic tumor exocrine pancreatic carcinoma glioblastoma large cell medulloblastoma lung carcinoma Malignant neoplasm of kidney non-small cell lung carcinoma Pick disease primitive neuroectodermal tumor tuberculosis atypical teratoid rhabdoid tumor gastric cancer kidney cancer lung adenocarcinoma malignant ependymoma malignant pancreatic neoplasm

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.