4CYM | pdb_00004cym

Complex of human VARP-ANKRD1 with Rab32-GppCp

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)
C	d4cymc_	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	d4cymb_	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	d4cyma_	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)
D	SCOP2B Superfamily	Ankyrin repeat	8078419	3000154	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ankyrin repeat	8078419	3000154	SCOP2B (2022-06-29)
E	SCOP2 Family	Ankyrin repeat	8078418	4000366	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Ankyrin repeat	8078419	3000154	SCOP2 (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	CID	e4cymD1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)
F	CID	e4cymF1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)
E	CID	e4cymE1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)
C	CID	e4cymC1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)
B	CID	e4cymB1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)
A	CID	e4cymA1	A: alpha bundles	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: CID	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
F	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)
E	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	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	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	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
D, E, F	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat
A, B, C	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
D, E, F	ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 27	small GTPase binding protein binding binding enzyme binding GTPase 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 SNARE binding guanyl-nucleotide exchange factor activity	localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development cellular process cellular response to stimulus cellular localization pigment cell differentiation response to stimulus developmental pigmentation cellular pigmentation endosome to pigment granule transport pigmentation establishment of localization in cell cellular pigment accumulation endosome to melanosome transport pigment accumulation intracellular transport response to external stimulus developmental maturation pigment granule maturation regulation of neuron projection development regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process positive regulation of neuron projection development positive regulation of cell projection organization positive regulation of cellular process regulation of biological process regulation of cell projection organization biological regulation regulation of plasma membrane bounded cell projection organization regulation of localization membrane fusion organelle membrane fusion negative regulation of biological process regulation of vesicle fusion negative regulation of vesicle fusion negative regulation of transport vesicle-mediated transport vesicle organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly negative regulation of cellular process protein-containing complex assembly SNARE complex assembly negative regulation of SNARE complex assembly membrane organization negative regulation of cellular component organization regulation of transport protein-containing complex organization regulation of vesicle-mediated transport regulation of cellular component biogenesis regulation of organelle organization negative regulation of protein-containing complex assembly organelle fusion organelle organization regulation of SNARE complex assembly negative regulation of organelle organization vesicle fusion endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of developmental process regulation of nervous system development positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol cell periphery plasma membrane transport vesicle endomembrane system lytic vacuole vacuole lysosome endosome tubular endosome cell projection neuron projection plasma membrane bounded cell projection cytoplasmic vesicle membrane vesicle membrane organelle membrane early endosome late endosome
A, B, C	RAS-RELATED PROTEIN RAB-32	GTP-dependent protein binding protein binding binding AP-3 adaptor complex binding protein-containing complex 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 GTP-dependent protein binding protein binding binding AP-3 adaptor complex binding protein-containing complex 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 AP-1 adaptor complex binding BLOC-2 complex binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	cellular component organization organelle organization cellular process cellular component organization or biogenesis phagosome maturation cellular response to stimulus cellular localization pigment cell differentiation response to stimulus cellular developmental process transport developmental pigmentation cellular pigmentation endosome to pigment granule transport cellular component organization organelle organization cellular process cellular component organization or biogenesis phagosome maturation cellular response to stimulus cellular localization pigment cell differentiation response to stimulus cellular developmental process transport developmental pigmentation cellular pigmentation endosome to pigment granule transport localization pigmentation cell differentiation establishment of localization in cell cellular pigment accumulation developmental process endosome to melanosome transport pigment accumulation intracellular transport response to external stimulus developmental maturation pigment granule maturation establishment of localization establishment of protein localization protein transport macromolecule localization intracellular protein localization intracellular protein transport vesicle organization melanosome organization pigment granule organization organelle assembly cellular component biogenesis cellular component assembly melanosome assembly localization within membrane protein localization to membrane vesicle-mediated transport antigen processing and presentation immune system process mitochondrion organization	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site membrane pigment granule intracellular vesicle cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site membrane pigment granule intracellular vesicle melanosome cytoplasmic vesicle vesicle cytosol phagocytic vesicle endocytic vesicle early endosome endosome phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network mitochondrial membrane organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane chitosome melanosome membrane pigment granule membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
D, E, F	IPR003123	VPS9 domain	Domain
D, E, F	IPR002110	Ankyrin repeat	Repeat
D, E, F	IPR051248	UPF0507/Ankyrin repeat domain-containing protein 27	Family
D, E, F	IPR037191	VPS9 domain superfamily	Homologous Superfamily
A, B, C	IPR030697	Ras-related protein Rab29/Rab38/Rab32	Family
A, B, C	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C	IPR005225	Small GTP-binding domain	Domain
A, B, C	IPR001806	Small GTPase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, E, F	Pharos: Q96NW4	eosinophilic esophagitis bipolar disorder malignant glioma myopathy dermatomyositis glioblastoma malignant mesothelioma ovarian cancer endogenous depression lymphoplasmacytic lymphoma medulloblastoma pancreatic ductal adenocarcinoma
A, B, C	Pharos: Q13637	leprosy allergic contact dermatitis HIV infectious disease Liver Cirrhosis, Experimental gastric carcinoma malignant ependymoma atypical teratoid rhabdoid tumor glioblastoma IgA glomerulonephritis lung cancer medulloblastoma fragile X syndrome lung carcinoma ovarian cancer

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.