4ITR | pdb_00004itr

Crystal Structure of IbpAFic2-H3717A in complex with adenylylated 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)
D	d4itrd_	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)
C	d4itrc_	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)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057416	3002022	SCOP2B (2022-06-29)
C	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)
D	Oxidored_q6	e4itrD1	A: alpha bundles	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: Oxidored_q6	ECOD (develop294)
C	ABC_tran	e4itrC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
B	Rrf2	e4itrB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: Rrf2	ECOD (develop294)
A	MR_MLE_N	e4itrA1	A: alpha bundles	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: MR_MLE_N	ECOD (develop294)

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	1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	CATH (4.3.0)
A	1.10.3290.10	Mainly Alpha	Orthogonal Bundle	Fic-like fold	Fido-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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, motili ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Cell division control protein 42 homolog	protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme 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 catalytic activity protein binding binding protein domain specific binding GBD domain binding thioesterase binding enzyme 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 catalytic activity ubiquitin-protein transferase activity signaling receptor binding apolipoprotein A-I receptor binding apolipoprotein receptor 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 identical protein binding 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 purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding kinase binding protein kinase binding G protein activity molecular function regulator activity	adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization membrane organization import into cell transport establishment of localization vesicle-mediated transport localization phagocytosis, engulfment membrane invagination adherens junction organization cellular component organization cell junction organization cellular process cellular component organization or biogenesis cell-cell junction organization membrane organization import into cell transport establishment of localization vesicle-mediated transport localization phagocytosis, engulfment membrane invagination phagocytosis endocytosis plasma membrane invagination 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 cell division cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis pseudopodium assembly cellular component assembly positive regulation of cell projection organization 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 dendritic cell migration leukocyte migration immune system process mononuclear cell migration cell migration cell motility establishment of organelle localization cellular localization nucleus localization intracellular transport organelle localization establishment of localization in cell nuclear migration 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 establishment of cell polarity establishment or maintenance of cell polarity 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 organelle organization actin cytoskeleton organization actin filament-based process cytoskeleton organization cellular response to stimulus cell surface receptor signaling pathway response to stimulus neuropilin signaling pathway signaling cell communication signal transduction developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate determination generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development neuron fate determination cell fate commitment system development Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway Wnt signaling pathway cell junction assembly biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cell projection morphogenesis neuron projection morphogenesis dendrite development dendritic spine morphogenesis synapse organization dendritic spine development dendritic spine organization postsynapse organization dendrite morphogenesis cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development neuron projection organization mitotic nuclear division organelle fission regulation of mitotic nuclear division regulation of organelle organization mitotic cell cycle regulation of mitotic cell cycle nuclear division mitotic cell cycle process regulation of nuclear division actin filament organization supramolecular fiber 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 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 regulation of cytoskeleton organization regulation of actin filament-based process regulation of actin filament bundle assembly actin filament bundle organization stress fiber assembly regulation of actin filament organization actomyosin structure organization regulation of stress fiber assembly contractile actin filament bundle assembly regulation of actomyosin structure organization regulation of actin cytoskeleton organization actin filament bundle assembly regulation of supramolecular fiber organization positive regulation of cell population proliferation respiratory tube development epithelial cell proliferation involved in lung morphogenesis lung development respiratory system development lung morphogenesis animal organ 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 animal organ development lung epithelium development tissue development regulation of cell population proliferation regulation of epithelial cell proliferation integrin-mediated signaling pathway heart development embryo development embryonic heart tube development circulatory system development embryonic organ development positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling polarized epithelial cell differentiation establishment of monopolar cell polarity establishment or maintenance of monopolar 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 tissue morphogenesis establishment or maintenance of epithelial cell apical/basal polarity establishment of apical/basal cell polarity establishment of epithelial cell polarity regulation of localization positive regulation of endocytosis regulation of endocytosis positive regulation of pinocytosis regulation of transport regulation of vesicle-mediated transport positive regulation of transport regulation of pinocytosis pinocytosis heart process system process circulatory system process heart contraction blood circulation positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus cellular response to type II interferon response to biotic stimulus response to peptide response to chemical defense response to other organism response to stress innate immune response cellular response to cytokine stimulus response to external biotic stimulus 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 cardiac conduction system development cardiac muscle tissue development striated muscle tissue development muscle tissue development filopodium assembly 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 locomotion 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 regulation of filopodium assembly positive regulation of filopodium assembly lamellipodium assembly regulation of lamellipodium assembly regulation of lamellipodium organization lamellipodium organization positive regulation of lamellipodium assembly positive regulation of lamellipodium organization macromolecule localization intracellular protein localization positive regulation of organelle organization positive regulation of actin filament bundle assembly positive regulation of stress fiber assembly positive regulation of cytoskeleton organization positive regulation of supramolecular fiber organization small GTPase-mediated signal transduction 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	cellular anatomical structure membrane apical part of cell cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone cellular anatomical structure membrane apical part of cell cell-cell junction anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle midzone microtubule cytoskeleton extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoplasm cytosol somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection synapse glutamatergic synapse Golgi transport complex protein-containing complex Golgi apparatus intracellular membrane-bounded organelle endomembrane system vesicle tethering complex Golgi membrane bounding membrane of organelle organelle membrane storage vacuole vacuole cell body neuronal cell body postsynapse actin-based cell projection filopodium midbody focal adhesion cell-substrate junction centrosome microtubule organizing center intracellular vesicle phagocytic vesicle cytoplasmic vesicle endocytic vesicle cell periphery plasma membrane mitotic spindle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule cell leading edge leading edge membrane
A, B	Adenosine monophosphate-protein transferase and cysteine protease IbpA	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity adenylyltransferase activity transferase activity nucleotidyltransferase activity AMPylase activity transferase activity, transferring phosphorus-containing groups	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process proteolysis protein nucleotidylation protein adenylylation negative regulation of hydrolase activity regulation of biological process negative regulation of GTPase activity regulation of catalytic activity macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process proteolysis protein nucleotidylation protein adenylylation negative regulation of hydrolase activity regulation of biological process negative regulation of GTPase activity regulation of catalytic activity biological regulation negative regulation of molecular function negative regulation of biological process negative regulation of catalytic activity regulation of GTPase activity regulation of molecular function regulation of hydrolase activity symbiont-mediated suppression of host immunoglobulin-mediated immune response symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	cellular anatomical structure extracellular region cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR003578	Small GTPase Rho	Family
C, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR037874	Cdc42	Family
C, D	IPR005225	Small GTP-binding domain	Domain
C, D	IPR001806	Small GTPase	Family
A, B	IPR012334	Pectin lyase fold	Homologous Superfamily
A, B	IPR024973	ESPR domain	Domain
A, B	IPR036597	Fido-like domain superfamily	Homologous Superfamily
A, B	IPR006473	Peptidase C58, YopT-type domain	Domain
A, B	IPR003812	Fido domain	Domain
A, B	IPR008638	Filamentous haemagglutinin FhaB/tRNA nuclease CdiA-like, TPS domain	Domain
A, B	IPR040198	Fido domain-containing protein	Family
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR025157	Hemagglutinin repeat	Repeat
A, B	IPR003951	Peptidase C58, Yersinia/Haemophilus virulence surface antigen	Family
A, B	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	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 atrial fibrillation undifferentiated carcinoma 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 atrial fibrillation undifferentiated carcinoma gastric cancer hepatocellular carcinoma lymphatic system disease malignant glioma oligodendroglioma adrenal gland cancer pilocytic astrocytoma schizophrenia atypical teratoid rhabdoid tumor uterine corpus leiomyoma gastric carcinoma large cell medulloblastoma medulloblastoma ovarian cancer plasma cell myeloma astrocytic tumor subependymal giant cell astrocytoma cancer endometriosis glioblastoma

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.