7KDC | pdb_00007kdc

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057504	3002022	SCOP2B (2022-06-29)
A	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)
D	LbH_EIF2B	e7kdcD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: LbH_EIF2B	ECOD (v294.1)
C	Ras	e7kdcC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ras	ECOD (v294.1)
B	LbH_EIF2B	e7kdcB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: LbH_EIF2B	ECOD (v294.1)
A	Ras	e7kdcA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Ras	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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, 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	Plexin-B2	molecular transducer activity signaling receptor activity transmembrane 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 cellular response to stimulus negative regulation of translation in response to stress response to stimulus negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation regulation of translation in response to stress cellular response to stress response to stress negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process 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 positive regulation of protein metabolic process positive regulation of translation positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of gene expression cytoplasmic translation cell surface receptor signaling pathway semaphorin-plexin signaling pathway signaling cell communication signal transduction protein phosphorylation regulation of protein modification process regulation of protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process protein modification process phosphorus metabolic process cell adhesion cell-cell adhesion homophilic cell-cell adhesion regulation of molecular function regulation of catalytic activity regulation of hydrolase activity regulation of GTPase activity negative regulation of tRNA metabolic process nucleobase-containing compound metabolic process regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process tRNA decay RNA catabolic process nucleobase-containing compound catabolic process tRNA metabolic process tRNA stabilization regulation of tRNA metabolic process nucleic acid catabolic process negative regulation of RNA metabolic process negative regulation of tRNA catabolic process catabolic process RNA metabolic process macromolecule catabolic process regulation of tRNA stability negative regulation of catabolic process negative regulation of RNA catabolic process regulation of catabolic process nucleic acid metabolic process RNA stabilization regulation of tRNA catabolic process regulation of RNA stability localization import into cell transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport regulation of cell adhesion negative regulation of cell adhesion	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex semaphorin receptor complex signaling receptor complex extracellular matrix external encapsulating structure extracellular region
A, B	Rho-related GTP-binding protein RhoD	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 protein 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 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 cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization protein polymerization actin polymerization or depolymerization actin filament polymerization protein-containing complex organization actin filament organization protein-containing complex assembly supramolecular fiber organization positive regulation of cell adhesion positive regulation of biological process positive regulation of cellular process response to fibroblast growth factor cellular response to stimulus cellular response to growth factor stimulus response to stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus fibroblast growth factor receptor signaling pathway response to growth factor signal transduction cellular response to fibroblast growth factor stimulus enzyme-linked receptor protein signaling pathway localization establishment of protein localization protein targeting establishment of localization 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 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 Rho protein signal transduction actin filament bundle organization actin filament bundle assembly	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane 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 endosome membrane cytoplasmic vesicle membrane vesicle membrane mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR057533	Plexin-B, PSI domain	Domain
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
A, B	IPR003578	Small GTPase Rho	Family
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR005225	Small GTP-binding domain	Domain
A, B	IPR001806	Small GTPase	Family

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.