3BH6

Crystal structure of the RP2-Arl3 complex bound to GppNHp

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3bh6a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	ADP-ribosylation factor	house 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	8057426	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	e3bh6A1	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	TBCC	e3bh6B7	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: C-CAP/cofactor C-like (From Topology)	T: C-CAP/cofactor C-like	F: TBCC	ECOD (1.6)
B	NDK	e3bh6B8	A: a+b two layers	X: Alpha-beta plaits	H: Nucleoside diphosphate kinases (From Topology)	T: Nucleoside diphosphate kinases	F: NDK	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	2.160.20.70	Mainly Beta	3 Solenoid	Pectate Lyase C-like		CATH (4.3.0)
B	3.30.70.141	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Nucleoside diphosphate kinase-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain
B	PF07986	Tubulin binding cofactor C (TBCC)	Tubulin binding cofactor C	Members of this family are involved in the folding pathway of tubulins and form a beta helix structure [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ADP-ribosylation factor-like protein 3	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 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 cation binding magnesium ion binding metal ion binding cytoskeletal protein binding microtubule binding protein binding tubulin binding GDP 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	protein localization localization cellular localization protein localization to cilium protein localization to organelle cellular macromolecule localization macromolecule localization cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling protein localization localization cellular localization protein localization to cilium protein localization to organelle cellular macromolecule localization macromolecule localization cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation smoothened signaling pathway cell communication signal transduction Golgi to plasma membrane transport post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane Golgi vesicle transport mitotic cell cycle process cytoskeleton-dependent cytokinesis mitotic cytokinesis cytokinesis cell division cell cycle mitotic cell cycle cell cycle process establishment of protein localization nitrogen compound transport organic substance transport protein transport organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization cell projection assembly developmental process multicellular organismal process cellular developmental process photoreceptor cell differentiation cell development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation neuron development anatomical structure development photoreceptor cell development system development intracellular transport protein-containing complex localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process intraciliary transport small GTPase-mediated signal transduction intracellular signal transduction intracellular signaling cassette protein localization to cell periphery protein localization to membrane protein localization to ciliary membrane animal organ development kidney development renal system development	membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection midbody intracellular anatomical structure axoneme ciliary plasm cytoplasmic region plasma membrane bounded cell projection cytoplasm intracellular organelle cytoskeleton membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection midbody intracellular anatomical structure axoneme ciliary plasm cytoplasmic region plasma membrane bounded cell projection cytoplasm intracellular organelle cytoskeleton intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle ciliary transition zone non-motile cilium 9+0 non-motile cilium neuron projection photoreceptor cell cilium photoreceptor connecting cilium centrosome microtubule organizing center microtubule cytoskeleton nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen Golgi apparatus endomembrane system Golgi membrane membrane bounding membrane of organelle organelle membrane polymeric cytoskeletal fiber cytoplasmic microtubule supramolecular fiber microtubule supramolecular polymer supramolecular complex spindle spindle microtubule ciliary basal body
B	Protein XRP2	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity 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 cation binding magnesium ion binding metal ion binding unfolded protein binding protein binding	localization post-Golgi vesicle-mediated transport transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation localization post-Golgi vesicle-mediated transport transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process protein metabolic process macromolecule metabolic process protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization organelle assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization organelle organization cellular component assembly cilium assembly cellular component organization or biogenesis cilium organization cell projection assembly multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception	membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle membrane-bounded organelle cell projection organelle cilium cellular anatomical entity plasma membrane bounded cell projection extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle microtubule organizing center intracellular anatomical structure cytoskeleton intracellular non-membrane-bounded organelle centriole microtubule cytoskeleton non-membrane-bounded organelle cell periphery plasma membrane membrane cytoplasm nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen cytoplasmic vesicle intracellular vesicle Golgi apparatus endomembrane system plasma membrane region periciliary membrane compartment nuclear body ciliary basal body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR044612	ADP-ribosylation factor-like protein 2/3	Family
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR005225	Small GTP-binding protein domain	Domain
A	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
B	IPR039093	Protein XRP2	Family
B	IPR017901	C-CAP/cofactor C-like domain	Domain
B	IPR012945	Tubulin binding cofactor C-like domain	Domain
B	IPR036223	Adenylate cyclase-associated CAP, C-terminal superfamily	Homologous Superfamily
B	IPR006599	CARP motif	Domain
B	IPR016098	Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal	Homologous Superfamily
B	IPR036850	Nucleoside diphosphate kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: O75695	retinitis pigmentosa retinitis pigmentosa 2 polycystic ovary syndrome adenoma breast carcinoma lung cancer medulloblastoma Sjogren syndrome astrocytic tumor cone-rod dystrophy malignant ependymoma oligodendroglioma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma retinitis pigmentosa retinitis pigmentosa 2 polycystic ovary syndrome adenoma breast carcinoma lung cancer medulloblastoma Sjogren syndrome astrocytic tumor cone-rod dystrophy malignant ependymoma oligodendroglioma primitive neuroectodermal tumor atypical teratoid rhabdoid tumor glioblastoma malignant glioma pilocytic astrocytoma retinal degeneration Sclerocystic Ovaries

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.