2REX | pdb_00002rex

Crystal structure of the effector domain of PLXNB1 bound with Rnd1 GTPase

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	d2rexa_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Rho GTPase binding domain	Plexin-B1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2rexc_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Rho GTPase binding domain	Plexin-B1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2rexb_	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)
D	d2rexd_	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)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057508	3002022	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8057508	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	Plexin_cytopl_2nd	e2rexA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
C	Plexin_cytopl_2nd	e2rexC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Plexin_cytopl_2nd	ECOD (1.6)
B	Ras	e2rexB1	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)
D	Ras	e2rexD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	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)
D	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
B, 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
A, C	Plexin-B1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity GTPase activating protein binding protein binding binding pyrophosphatase activity enzyme regulator activity GTPase activity molecular function activator activity nucleoside-triphosphatase regulator activity hydrolase activity GTPase regulator activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity GTPase activating protein binding protein binding binding pyrophosphatase activity enzyme regulator activity GTPase activity molecular function activator activity nucleoside-triphosphatase regulator activity hydrolase activity GTPase regulator activity enzyme activator activity ribonucleoside triphosphate phosphatase activity GTPase activator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides molecular function regulator activity hydrolase activity, acting on acid anhydrides catalytic activity semaphorin receptor binding signaling receptor binding	positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity multicellular organismal process 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 multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of biological process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis 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 axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development cellular process regulation of plasma membrane bounded cell projection organization cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling 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 regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization cell migration cell motility regulation of cell motility regulation of locomotion regulation of cell migration locomotion regulation of cell shape regulation of cell morphogenesis regulation of biological quality negative regulation of cell population proliferation cell population proliferation negative regulation of biological process osteoblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of osteoblast proliferation regulation of osteoblast proliferation cell surface receptor signaling pathway semaphorin-plexin signaling pathway bone maturation animal organ development developmental maturation skeletal system development ossification anatomical structure maturation ossification involved in bone maturation animal organ maturation bone development inhibitory synapse assembly cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly cell adhesion regulation of cell adhesion negative regulation of cell adhesion	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex semaphorin receptor complex receptor complex glutamatergic synapse extracellular region
B, D	Rho-related GTP-binding protein Rho6	protein binding binding signaling receptor binding kinase binding enzyme binding protein kinase binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding protein binding binding signaling receptor binding kinase binding enzyme binding protein kinase 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 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	developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development neuron maturation cellular process cell maturation system development regulation of cytoskeleton organization regulation of biological process regulation of cellular component organization regulation of cellular process regulation of actin filament-based process actin cytoskeleton organization biological regulation regulation of organelle organization cellular component organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization actin filament organization supramolecular fiber organization cell migration cell motility cellular response to stimulus response to stimulus signaling signal transduction cell communication small GTPase-mediated signal transduction intracellular signal transduction intracellular signaling cassette cell adhesion regulation of cell adhesion negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion	cell-cell junction adherens junction cellular anatomical structure anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell-cell junction adherens junction cellular anatomical structure anchoring junction cell junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane membrane-bounded organelle intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR002909	IPT domain	Domain
A, C	IPR041362	Plexin, TIG domain 2	Domain
A, C	IPR016201	PSI domain	Domain
A, C	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A, C	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, C	IPR002165	Plexin repeat	Repeat
A, C	IPR041019	Plexin, TIG domain 1	Domain
A, C	IPR031148	Plexin family	Family
A, C	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A, C	IPR036352	Sema domain superfamily	Homologous Superfamily
A, C	IPR001627	Sema domain	Domain
B, D	IPR005225	Small GTP-binding domain	Domain
B, D	IPR001806	Small GTPase	Family
B, D	IPR003578	Small GTPase Rho	Family
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: O43157	Neurodevelopmental Disorders astrocytic tumor osteosarcoma subependymal giant cell astrocytoma Down syndrome ovarian cancer malignant ependymoma oligodendroglioma prostate cancer
B, D	Pharos: Q92730	astrocytic tumor large cell medulloblastoma malignant glioma oligodendroglioma psoriasis atypical teratoid rhabdoid tumor lung cancer medulloblastoma pilocytic astrocytoma glioblastoma malignant ependymoma non-small cell lung carcinoma primitive neuroectodermal tumor

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.