4OJK | pdb_00004ojk

Structure of the cGMP Dependent Protein Kinase II and Rab11b Complex

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	d4ojka1	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	d4ojka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4ojkb1	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	d4ojkb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8057278	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8057278	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	e4ojkA1	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	Ras	e4ojkB1	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	3.40.50.300	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)

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, 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, B	Ras-related protein Rab-11B	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 GDP binding cell adhesion molecule binding cadherin binding protein binding cytoskeletal protein binding myosin V binding myosin 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	receptor metabolic process metabolic process cellular process macromolecule metabolic process receptor recycling regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of transport transport biological regulation intracellular transport localization within membrane receptor metabolic process metabolic process cellular process macromolecule metabolic process receptor recycling regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of transport transport biological regulation intracellular transport localization within membrane regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane localization regulation of cellular localization establishment of localization in cell regulation of endocytic recycling regulation of intracellular transport protein localization to cell surface regulation of protein localization macromolecule localization regulation of protein localization to cell surface intracellular protein localization cellular response to stimulus response to stimulus response to pH cellular response to pH response to abiotic stimulus cellular response to acidic pH response to acidic pH cellular response to abiotic stimulus cellular response to environmental stimulus regulation of monoatomic ion transport regulation of monoatomic anion transport monoatomic anion transport monoatomic ion transport establishment of protein localization nitrogen compound transport cell communication carbohydrate homeostasis regulation of biological quality regulation of hormone levels establishment of protein localization to extracellular region intracellular glucose homeostasis protein secretion cellular response to oxygen-containing compound cellular response to carbohydrate stimulus chemical homeostasis response to glucose response to chemical glucose homeostasis insulin secretion involved in cellular response to glucose stimulus signaling homeostatic process hormone secretion protein localization to extracellular region peptide secretion secretion by cell response to monosaccharide response to carbohydrate amide transport signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus secretion cell-cell signaling export from cell response to oxygen-containing compound cellular response to glucose stimulus peptide transport response to hexose cellular response to chemical stimulus cellular homeostasis protein transport peptide hormone secretion hormone transport insulin secretion regulated exocytosis exocytosis vesicle localization establishment of organelle localization establishment of melanosome localization establishment of vesicle localization cellular pigmentation pigment granule transport establishment of pigment granule localization pigmentation pigment granule localization organelle localization melanosome transport melanosome localization constitutive secretory pathway establishment of protein localization to membrane multicellular organismal process amyloid-beta clearance amyloid-beta clearance by transcytosis transcytosis iron ion transport metal ion transport transferrin transport transition metal ion transport monoatomic cation transport	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular vesicle phagocytic vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle endocytic vesicle membrane phagocytic vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane endocytic vesicle membrane organelle membrane endosome membrane endosome recycling endosome endomembrane system recycling endosome membrane Golgi apparatus synapse transport vesicle membrane presynapse synaptic vesicle synaptic vesicle membrane cell junction transport vesicle exocytic vesicle membrane secretory vesicle exocytic vesicle
C, D	cGMP-dependent protein kinase 2	guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cGMP binding guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding cGMP binding small molecule binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity protein serine kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups adenyl ribonucleotide binding purine ribonucleoside triphosphate binding adenyl nucleotide binding ATP binding protein binding kinase binding enzyme binding protein kinase binding mitogen-activated protein kinase binding protein serine/threonine kinase activity cyclic nucleotide-dependent protein kinase activity cGMP-dependent protein kinase activity identical protein binding	rhythmic process circadian rhythm multicellular organismal process regulation of cartilage development regulation of chondrocyte differentiation regulation of cellular process regulation of developmental process connective tissue development cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process multicellular organism development rhythmic process circadian rhythm multicellular organismal process regulation of cartilage development regulation of chondrocyte differentiation regulation of cellular process regulation of developmental process connective tissue development cellular developmental process positive regulation of biological process regulation of cell differentiation positive regulation of chondrocyte differentiation positive regulation of developmental process multicellular organism development skeletal system development positive regulation of cell differentiation cell differentiation anatomical structure development regulation of multicellular organismal process positive regulation of cellular process system development developmental process regulation of multicellular organismal development regulation of biological process biological regulation animal organ development tissue development chondrocyte differentiation positive regulation of multicellular organismal process positive regulation of cartilage development cellular process cartilage development localization protein localization to cell periphery cellular localization protein localization to plasma membrane macromolecule localization intracellular protein localization localization within membrane protein localization to membrane cellular response to stimulus response to stimulus signaling signal transduction cell communication regulation of biosynthetic process circadian regulation of gene expression regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of cellular component size homeostatic process cell volume homeostasis cellular component organization negative regulation of cell volume cellular homeostasis cellular component organization or biogenesis regulation of biological quality regulation of cell size regulation of anatomical structure size regulation of localization negative regulation of monoatomic anion transport transport regulation of transport negative regulation of monoatomic ion transport regulation of monoatomic ion transport negative regulation of biological process negative regulation of transport establishment of localization chloride transport negative regulation of chloride transport monoatomic anion transport regulation of monoatomic anion transport monoatomic ion transport regulation of chloride transport inorganic anion transport regulation of protein localization positive regulation of protein localization response to osmotic stress cellular hypotonic response cellular response to chemical stress cellular response to osmotic stress cellular response to environmental stimulus hypotonic response cellular response to chemical stimulus cellular response to stress response to stress response to chemical response to abiotic stimulus cellular response to abiotic stimulus	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure nuclear membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope organelle nuclear envelope organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A, B	IPR050209	Rab GTPases family involved in membrane trafficking	Family
C, D	IPR017441	Protein kinase, ATP binding site	Binding Site
C, D	IPR014710	RmlC-like jelly roll fold	Homologous Superfamily
C, D	IPR018488	Cyclic nucleotide-binding, conserved site	Conserved Site
C, D	IPR000719	Protein kinase domain	Domain
C, D	IPR000961	AGC-kinase, C-terminal	Domain
C, D	IPR000595	Cyclic nucleotide-binding domain	Domain
C, D	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
C, D	IPR002374	cGMP-dependent kinase	Family
C, D	IPR018490	Cyclic nucleotide-binding domain superfamily	Homologous Superfamily
C, D	IPR035014	cGMP-dependent protein kinase, catalytic domain	Domain
C, D	IPR008271	Serine/threonine-protein kinase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q15907	HIV infectious disease atypical teratoid rhabdoid tumor heart disease intellectual disability metabolic syndrome X psoriasis Epileptic encephalopathy leukodystrophy neurodevelopmental disorder with ataxic gait, absent speech, and decreased cortical white matter rectal cancer glioblastoma medulloblastoma 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.