4DID

Crystal structure of Salmonella effector N-terminal domain SopB in complex with Cdc42

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)
A	d4dida_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	CDC42	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	Ras-like P-loop GTPases	8057416	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)
A	Ras	e4didA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
B	IpgD	e4didB1	A: alpha bundles	X: Inositol phosphate phosphatase sopB N-terminal domain (From Topology)	H: Inositol phosphate phosphatase sopB N-terminal domain (From Topology)	T: Inositol phosphate phosphatase sopB N-terminal domain	F: IpgD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	1.20.58.450	Mainly Alpha	Up-down Bundle	Methane Monooxygenase Hydroxylase	Chain G, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motil ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain
B	PF05925	Enterobacterial virulence protein IpgD (IpgD)	Enterobacterial virulence protein IpgD	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Cell division control protein 42 homolog	protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme 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 GTP-dependent protein binding protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme 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 GTP-dependent protein binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase binding protein kinase binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity ubiquitin-protein transferase activity signaling receptor binding apolipoprotein A-I receptor binding apolipoprotein receptor binding mitogen-activated protein kinase kinase kinase binding identical protein binding G protein activity molecular function regulator activity	regulation of cytokinesis regulation of biological process regulation of cellular process positive regulation of cell division regulation of cell cycle process biological regulation positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cellular process cell division regulation of cytokinesis regulation of biological process regulation of cellular process positive regulation of cell division regulation of cell cycle process biological regulation positive regulation of biological process cytokinesis positive regulation of cell cycle regulation of cell division positive regulation of cytokinesis positive regulation of cell cycle process cellular process cell division cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process protein localization localization cellular localization cellular macromolecule localization macromolecule localization regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization pseudopodium assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization establishment of organelle localization transport nucleus localization intracellular transport establishment of localization organelle localization establishment of localization in cell nuclear migration positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion cell-substrate adhesion cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading cellular response to stimulus cell surface receptor signaling pathway response to stimulus neuropilin signaling pathway signaling cell communication signal transduction multicellular organismal process cellular developmental process plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation anatomical structure development dendritic spine morphogenesis synapse organization system development developmental process dendritic spine development dendritic spine organization postsynapse organization dendrite morphogenesis nervous system development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis cell junction organization neuron development neuron projection organization gland development animal organ development salivary gland development gland morphogenesis salivary gland morphogenesis anatomical structure formation involved in morphogenesis animal organ morphogenesis exocrine system development submandibular salivary gland formation organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization regulation of postsynapse organization regulation of synapse organization regulation of synapse structure or activity regulation of biological quality attachment of spindle microtubules to kinetochore metaphase chromosome alignment chromosome localization nuclear chromosome segregation regulation of attachment of spindle microtubules to kinetochore establishment of chromosome localization chromosome segregation organelle transport along microtubule microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process Golgi localization establishment of Golgi localization regulation of growth growth positive regulation of cell growth regulation of cell growth cell growth positive regulation of growth positive regulation of cell population proliferation respiratory tube development epithelial cell proliferation involved in lung morphogenesis lung development respiratory system development lung morphogenesis epithelial cell proliferation regulation of epithelial cell proliferation involved in lung morphogenesis epithelium development cell population proliferation positive regulation of epithelial cell proliferation involved in lung morphogenesis tube development positive regulation of epithelial cell proliferation lung epithelium development tissue development regulation of cell population proliferation regulation of epithelial cell proliferation regulation of cytoskeleton organization regulation of actin filament-based process regulation of organelle organization regulation of actin cytoskeleton organization regulation of synapse structural plasticity positive regulation of synapse structural plasticity polarized epithelial cell differentiation establishment of monopolar cell polarity establishment or maintenance of monopolar cell polarity establishment or maintenance of cell polarity epithelial cell differentiation morphogenesis of a polarized epithelium establishment or maintenance of apical/basal cell polarity establishment or maintenance of bipolar cell polarity establishment of epithelial cell apical/basal polarity morphogenesis of an epithelium establishment of cell polarity tissue morphogenesis establishment or maintenance of epithelial cell apical/basal polarity establishment of apical/basal cell polarity establishment of epithelial cell polarity heart process system process circulatory system process heart contraction blood circulation response to organic substance biological process involved in interspecies interaction between organisms response to type II interferon response to cytokine cellular response to type II interferon response to biotic stimulus response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus cellular response to organic substance immune response response to other organism defense response defense response to symbiont response to external stimulus cellular response to chemical stimulus response to chemical immune system process defense response to other organism head development brain development substantia nigra development central nervous system development midbrain development neural nucleus development myeloid leukocyte differentiation hemopoiesis macrophage differentiation mononuclear cell differentiation myeloid cell differentiation leukocyte differentiation positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion filopodium assembly regulation of filopodium assembly positive regulation of filopodium assembly modification of synaptic structure regulation of lamellipodium assembly regulation of lamellipodium organization lamellipodium assembly positive regulation of lamellipodium assembly positive regulation of lamellipodium organization lamellipodium organization positive regulation of organelle organization regulation of actin filament bundle assembly positive regulation of actin filament bundle assembly actin filament bundle organization positive regulation of stress fiber assembly stress fiber assembly regulation of actin filament organization actomyosin structure organization positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of supramolecular fiber organization endothelin receptor signaling pathway involved in heart process endothelin receptor signaling pathway G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway involved in heart process Golgi organization endomembrane system organization adherens junction organization cell-cell junction organization membrane organization import into cell vesicle-mediated transport phagocytosis, engulfment membrane invagination phagocytosis endocytosis plasma membrane invagination actin filament branching dendritic cell migration leukocyte migration mononuclear cell migration positive regulation of DNA replication regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process organic cyclic compound metabolic process DNA replication positive regulation of DNA metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death regulation of neuron apoptotic process negative regulation of cellular component organization protein-containing complex organization negative regulation of biological process negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly protein-containing complex assembly negative regulation of cellular process blood vessel morphogenesis angiogenesis sprouting angiogenesis vasculature development circulatory system development tube morphogenesis blood vessel development neuron fate commitment cell fate determination neuron fate determination cell fate commitment positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway Wnt signaling pathway cell junction assembly mitotic nuclear division organelle fission regulation of mitotic nuclear division mitotic cell cycle regulation of mitotic cell cycle nuclear division mitotic cell cycle process regulation of nuclear division small GTPase-mediated signal transduction Cdc42 protein signal transduction Rho protein signal transduction regulation of localization establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport positive regulation of intracellular transport regulation of intracellular transport regulation of transport organic substance transport regulation of establishment of protein localization regulation of protein transport positive regulation of transport protein transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport regulation of modification of synaptic structure regulation of modification of postsynaptic structure modification of postsynaptic structure integrin-mediated signaling pathway modulation by host of viral process modulation by host of symbiont process biological process involved in interaction with symbiont biological process involved in symbiotic interaction heart development embryo development embryonic heart tube development embryonic organ development regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of endocytosis regulation of endocytosis positive regulation of pinocytosis regulation of vesicle-mediated transport regulation of pinocytosis pinocytosis cardiac conduction system development cardiac muscle tissue development striated muscle tissue development muscle tissue development heart morphogenesis cardiac neural crest cell development involved in heart development neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration neural crest cell migration stem cell development cardiac neural crest cell development involved in outflow tract morphogenesis neural crest cell differentiation cell migration involved in heart development cardiocyte differentiation stem cell differentiation cardiac neural crest cell differentiation involved in heart development outflow tract morphogenesis mesenchymal cell differentiation cardiac neural crest cell migration involved in outflow tract morphogenesis	cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cell-cell junction anchoring junction cell junction cellular anatomical entity intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle Golgi membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle organelle membrane neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree midbody focal adhesion cell-substrate junction intracellular vesicle phagocytic vesicle cytoplasmic vesicle vesicle endocytic vesicle cell periphery plasma membrane protein-containing complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane intracellular non-membrane-bounded organelle cytoplasmic ribonucleoprotein granule supramolecular complex non-membrane-bounded organelle ribonucleoprotein granule Schaffer collateral - CA1 synapse cell leading edge leading edge membrane apical part of cell cytoskeleton spindle spindle midzone microtubule cytoskeleton extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle secretory granule secretory vesicle glutamatergic synapse Golgi transport complex vesicle tethering complex storage vacuole vacuole cell body neuronal cell body actin-based cell projection filopodium centrosome microtubule organizing center mitotic spindle
B	Inositol phosphate phosphatase sopB	molecular function activator activity molecular function regulator activity phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds lipid phosphatase activity phosphatase activity hydrolase activity catalytic activity	regulation of signaling regulation of biological process negative regulation of signaling signaling biological regulation negative regulation of biological process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of signaling regulation of biological process negative regulation of signaling signaling biological regulation negative regulation of biological process positive regulation of DNA replication positive regulation of biological process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of nucleobase-containing compound metabolic process primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process organic cyclic compound metabolic process DNA replication positive regulation of DNA metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process regulation of DNA replication regulation of growth regulation of cellular component organization regulation of cellular process growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular process cellular component organization or biogenesis regulation of protein modification process regulation of catalytic activity regulation of protein phosphorylation regulation of transferase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process regulation of protein kinase activity regulation of molecular function regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process	cell periphery cellular anatomical entity membrane-bounded organelle host cellular component host intracellular part extracellular organelle extracellular region host cell cytoplasm part symbiont-containing vacuole host cell cytoplasm host cell part organelle host intracellular region extracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001806	Small GTPase	Family
A	IPR003578	Small GTPase Rho	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR037874	Cdc42	Family
A	IPR005225	Small GTP-binding protein domain	Domain
B	IPR008108	Phosphatase IpgD/SopB	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P60953	macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome Necrosis sarcomatoid carcinoma carcinoma intellectual disability HIV infectious disease lung cancer malignant ependymoma mammary neoplasms, animal Pick disease undifferentiated carcinoma atrial fibrillation gastric cancer hepatocellular carcinoma lymphatic system disease macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome Necrosis sarcomatoid carcinoma carcinoma intellectual disability HIV infectious disease lung cancer malignant ependymoma mammary neoplasms, animal Pick disease undifferentiated carcinoma atrial fibrillation gastric cancer hepatocellular carcinoma lymphatic system disease malignant glioma oligodendroglioma pilocytic astrocytoma adrenal gland cancer schizophrenia uterine corpus leiomyoma atypical teratoid rhabdoid tumor gastric carcinoma large cell medulloblastoma medulloblastoma ovarian cancer plasma cell myeloma subependymal giant cell astrocytoma astrocytic tumor cancer endometriosis glioblastoma

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.