7KDC

The complex between RhoD and the Plexin B2 RBD

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d7kdca_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d7kdcb_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d7kdcc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d7kdcd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	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	8057504	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057504	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	PF00071	e7kdcA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
B	PF00071	e7kdcB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00071	ECOD (1.6)
C	PF20170	e7kdcC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20170	ECOD (1.6)
D	PF20170	e7kdcD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF20170	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
C, D	PF20170	Plexin cytoplasmic RhoGTPase-binding domain (Plexin_RBD)	Plexin cytoplasmic RhoGTPase-binding domain	This entry represents the RhoGTPase-binding domain found in the cytoplasmic domain of plexins [1].	Domain
C, D	PF08337	Plexin cytoplasmic RasGAP domain (Plexin_cytopl)	Plexin cytoplasmic RasGAP domain	This family features the C-terminal regions of various plexins (e.g. Swiss:P51805). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels [1,2]. The cytop ...	This family features the C-terminal regions of various plexins (e.g. Swiss:P51805). Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels [1,2]. The cytoplasmic region, which has been called a SEX domain in some members of this family [3], is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins [4]. This domain acts as a RasGAP domain [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Rho-related GTP-binding protein RhoD	protein binding binding kinase binding enzyme binding protein kinase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding protein binding binding kinase binding enzyme binding protein kinase binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity 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 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	regulation of biological process cell adhesion regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cellular process positive regulation of cellular process lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization regulation of biological process cell adhesion regulation of cellular process positive regulation of cell adhesion regulation of cell adhesion biological regulation positive regulation of biological process cellular process positive regulation of cellular process lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis cellular component assembly lamellipodium organization cellular component organization or biogenesis cell projection 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 cell migration cell motility locomotion cellular response to stimulus regulation of signaling small GTPase-mediated signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication signal transduction focal adhesion assembly cell-substrate junction assembly cell-substrate adhesion cell junction organization cell-matrix adhesion cell junction assembly cell-substrate junction organization Rho protein signal transduction organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization actin filament bundle organization actin filament bundle assembly	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle Golgi membrane membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane cytosol endosome membrane cytoplasmic vesicle membrane vesicle membrane mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane
C, D	Plexin-B2	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity	developmental process multicellular organismal process nervous system development excitatory synapse assembly cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development cellular process synapse organization cellular component organization or biogenesis developmental process multicellular organismal process nervous system development excitatory synapse assembly cellular component organization cellular component biogenesis multicellular organism development cell junction organization cellular component assembly cell junction assembly anatomical structure development cellular process synapse organization cellular component organization or biogenesis synapse assembly system development neuroblast proliferation cell population proliferation cellular developmental process generation of neurons neurogenesis cell differentiation neural precursor cell proliferation head development central nervous system development animal organ development brain development positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis positive regulation of cell projection organization regulation of biological process regulation of cell projection organization positive regulation of cell development positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis regulation of nervous system development positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization biological regulation axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development regulation of plasma membrane bounded cell projection organization regulation of cell motility neuron migration regulation of neuron migration regulation of locomotion regulation of cell migration cell migration cell motility locomotion positive regulation of neuron projection development regulation of cell shape regulation of cell morphogenesis regulation of biological quality embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure cellular biosynthetic process positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of translation positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process regulation of biosynthetic process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction regulation of protein modification process regulation of protein phosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process protein modification process phosphorus metabolic process protein phosphorylation phosphorylation macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process cell adhesion cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules homophilic cell adhesion via plasma membrane adhesion molecules regulation of molecular function regulation of catalytic activity regulation of hydrolase activity regulation of GTPase activity regulation of cell adhesion negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion semaphorin-plexin signaling pathway involved in neuron projection guidance semaphorin-plexin signaling pathway involved in axon guidance axon guidance neuron projection guidance	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity plasma membrane membrane protein-containing complex semaphorin receptor complex receptor complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001806	Small GTPase	Family
A, B	IPR003578	Small GTPase Rho	Family
A, B	IPR005225	Small GTP-binding protein domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C, D	IPR002909	IPT domain	Domain
C, D	IPR016201	PSI domain	Domain
C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C, D	IPR008936	Rho GTPase activation protein	Homologous Superfamily
C, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
C, D	IPR002165	Plexin repeat	Repeat
C, D	IPR041019	Plexin, TIG domain 1	Domain
C, D	IPR031148	Plexin family	Family
C, D	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
C, D	IPR036352	Sema domain superfamily	Homologous Superfamily
C, D	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O00212	esophageal adenocarcinoma psoriasis malignant mesothelioma osteosarcoma

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 R01GM133198.