5X3F | pdb_00005x3f

Crystal structure of the YgjG-Protein A-Zpa963-PKA catalytic domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Bacterial immunoglobulin/albumin-binding domains	8091639	3001373	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8098688	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein kinase-like (PK-like)	8040503	3000066	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	Brix	e5x3fA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
B	ECH_1	e5x3fB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Immunoglobulin-related	T: HAD-like	F: ECH_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (utative)
A	1.20.5.420	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Immunoglobulin FC, subunit C	CATH (utative)
B	3.30.200.20	Alpha Beta	2-Layer Sandwich	Phosphorylase Kinase	domain 1	CATH (4.3.0)
B	1.10.510.10	Mainly Alpha	Orthogonal Bundle	Transferase(Phosphotransferase)	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00202	Aminotransferase class-III (Aminotran_3)	Aminotransferase class-III		Domain
B	PF00069	Protein kinase domain (Pkinase)	Protein kinase domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putrescine aminotransferase,Immunoglobulin G-binding protein A	protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups diamine:2-oxoglutarate transaminase activity transaminase activity transferase activity catalytic activity putrescine:2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding binding immunoglobulin binding IgG binding transferase activity, transferring nitrogenous groups diamine:2-oxoglutarate transaminase activity transaminase activity transferase activity catalytic activity putrescine:2-oxoglutarate transaminase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding anion binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process catabolic process oxoacid metabolic process L-lysine catabolic process L-amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process polyamine metabolic process biogenic amine catabolic process amine metabolic process putrescine catabolic process putrescine metabolic process polyamine catabolic process biogenic amine metabolic process amine catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B	Zpa963,cAMP-dependent protein kinase catalytic subunit alpha	small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H1 kinase activity histone H1-4S35 kinase activity small GTPase binding protein binding binding enzyme binding GTPase binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups histone H1 kinase activity histone H1-4S35 kinase activity histone modifying activity catalytic activity histone kinase activity cation binding manganese ion binding transition metal ion binding ion binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein domain specific binding protein serine/threonine/tyrosine kinase activity cyclic nucleotide-dependent protein kinase activity cAMP-dependent protein kinase activity protein serine kinase activity magnesium ion binding kinase binding protein kinase binding protein kinase A binding protein kinase A regulatory subunit binding	developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation developmental process spermatid development spermatid differentiation sexual reproduction cellular developmental process spermatogenesis reproductive process multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism developmental maturation developmental process involved in reproduction gamete generation male gamete generation sperm capacitation anatomical structure maturation cell differentiation anatomical structure development germ cell development cellular process cell maturation cellular response to stimulus cellular response to heat response to stimulus cellular response to stress response to stress response to heat response to abiotic stimulus response to temperature stimulus cellular response to nutrient levels response to nutrient levels ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration regulation of cellular process negative regulation of small molecule metabolic process negative regulation of glycolytic process oxoacid metabolic process negative regulation of biological process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process negative regulation of ATP metabolic process regulation of primary metabolic process regulation of ATP metabolic process nucleobase-containing compound metabolic process regulation of purine nucleotide catabolic process negative regulation of nucleotide metabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process negative regulation of carbohydrate metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process regulation of carbohydrate catabolic process regulation of biological process negative regulation of metabolic process negative regulation of purine nucleotide catabolic process purine nucleoside diphosphate metabolic process primary metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process metabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process regulation of metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration catabolic process ATP metabolic process negative regulation of purine nucleotide metabolic process energy derivation by oxidation of organic compounds negative regulation of phosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process negative regulation of cellular process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process negative regulation of nucleotide catabolic process negative regulation of catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process biological regulation ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process negative regulation of phosphorus metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process TOR signaling signaling intracellular signal transduction cell communication signal transduction TORC1 signaling regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport positive regulation of biological process vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis neutral lipid metabolic process regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process regulation of lipid metabolic process glycerolipid catabolic process positive regulation of metabolic process triglyceride catabolic process positive regulation of lipid catabolic process triglyceride metabolic process positive regulation of lipid metabolic process lipid catabolic process neutral lipid catabolic process acylglycerol catabolic process regulation of lipid catabolic process positive regulation of catabolic process positive regulation of triglyceride catabolic process glycerolipid metabolic process acylglycerol metabolic process regulation of triglyceride catabolic process lipid metabolic process RNA metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process macromolecule metabolic process RNA processing multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis system development morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure trans-synaptic signaling regulation of signaling modulation of chemical synaptic transmission cell-cell signaling chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication postsynaptic modulation of chemical synaptic transmission regulation of protein metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic process protein catabolic process macromolecule catabolic process regulation of proteasomal protein catabolic process protein metabolic process regulation of protein catabolic process formation of primary germ layer mesoderm morphogenesis gastrulation mesoderm formation mesoderm development potassium ion homeostasis inorganic ion homeostasis homeostatic process cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis intracellular potassium ion homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of osteoblast differentiation regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification monosaccharide metabolic process gluconeogenesis positive regulation of biosynthetic process regulation of glucose metabolic process positive regulation of gluconeogenesis regulation of biosynthetic process small molecule biosynthetic process carbohydrate biosynthetic process hexose metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process regulation of gluconeogenesis positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process glucose metabolic process interleukin-2-mediated signaling pathway cell surface receptor signaling pathway cellular response to interleukin-2 response to cytokine cytokine-mediated signaling pathway response to peptide response to interleukin-2 response to chemical cellular response to cytokine stimulus response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus response to monosaccharide response to carbohydrate response to glucose glucose homeostasis carbohydrate homeostasis cellular response to hexose stimulus cellular response to monosaccharide stimulus cellular response to nitrogen compound response to endogenous stimulus response to peptide hormone cellular response to peptide hormone stimulus response to nitrogen compound response to glucagon cellular response to glucagon stimulus cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus regulation of steroid biosynthetic process regulation of cholesterol biosynthetic process regulation of cholesterol metabolic process steroid metabolic process sterol metabolic process cholesterol metabolic process lipid biosynthetic process alcohol metabolic process steroid biosynthetic process secondary alcohol biosynthetic process regulation of alcohol biosynthetic process regulation of steroid metabolic process cholesterol biosynthetic process positive regulation of cholesterol biosynthetic process secondary alcohol metabolic process positive regulation of steroid biosynthetic process sterol biosynthetic process positive regulation of lipid biosynthetic process regulation of sterol biosynthetic process alcohol biosynthetic process positive regulation of cholesterol metabolic process positive regulation of steroid metabolic process regulation of lipid biosynthetic process positive regulation of alcohol biosynthetic process positive regulation of sterol biosynthetic process bicellular tight junction assembly regulation of bicellular tight junction assembly tight junction organization apical junction assembly regulation of cellular component biogenesis cellular component biogenesis regulation of cell junction assembly cell junction organization cellular component assembly cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization negative regulation of signaling regulation of signal transduction negative regulation of cell communication negative regulation of smoothened signaling pathway regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction smoothened signaling pathway regulation of response to stimulus regulation of protein maturation protein maturation regulation of proteolysis proteolysis regulation of gene expression regulation of protein processing protein processing regulation of macromolecule biosynthetic process cellular localization regulated exocytosis synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport in synapse secretion by cell signal release establishment of localization in cell spontaneous exocytosis of neurotransmitter neurotransmitter secretion secretion export from cell neurotransmitter transport signal release from synapse exocytosis adenylate cyclase-activating G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation establishment of protein localization regulation of protein localization nucleocytoplasmic transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization positive regulation of protein transport intercellular transport positive regulation of intracellular transport intracellular protein localization nuclear export regulation of protein export from nucleus regulation of intracellular transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus positive regulation of protein export from nucleus protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport protein localization to organelle protein localization to lipid droplet cAMP/PKA signal transduction intracellular signaling cassette adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway cellular response to parathyroid hormone stimulus response to parathyroid hormone regulation of glycolytic process through fructose-6-phosphate negative regulation of glycolytic process through fructose-6-phosphate glycolytic process through fructose-6-phosphate negative regulation of intracellular signal transduction negative regulation of TORC1 signaling regulation of intracellular signal transduction negative regulation of TOR signaling regulation of TORC1 signaling regulation of TOR signaling cellular response to cold response to cold synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic cell cycle regulation of cell cycle regulation of cellular respiration regulation of meiotic cell cycle regulation of reproductive process meiotic cell cycle negative regulation of cell cycle negative regulation of reproductive process negative regulation of meiotic cell cycle	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle plasma membrane bounded cell projection intracellular organelle cell projection cellular anatomical structure cytoskeleton organelle membraneless organelle cytoplasm nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule nuclear body nucleoplasm organelle lumen supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytosol 9+2 motile cilium sperm flagellum motile cilium sperm midpiece synapse cell junction glutamatergic synapse neuromuscular junction perinuclear region of cytoplasm postsynapse acrosomal vesicle intracellular vesicle endomembrane system cytoplasmic vesicle secretory granule secretory vesicle vesicle mitochondrion centrosome microtubule organizing center microtubule cytoskeleton cell periphery plasma membrane membrane presynapse protein-containing complex lipid droplet ciliary base protein kinase complex transferase complex, transferring phosphorus-containing groups catalytic complex transferase complex intracellular protein-containing complex nucleotide-activated protein kinase complex cAMP-dependent protein kinase complex serine/threonine protein kinase complex membrane microdomain membrane raft plasma membrane raft plasma membrane region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR009063	Immunoglobulin/albumin-binding domain superfamily	Homologous Superfamily
A	IPR005877	YSIRK Gram-positive signal peptide	Domain
A	IPR036779	LysM domain superfamily	Homologous Superfamily
A	IPR005038	Octapeptide repeat	Repeat
A	IPR003132	Protein A, Ig-binding domain	Domain
A	IPR018392	LysM domain	Domain
A	IPR019931	LPXTG cell wall anchor motif	Conserved Site
A	IPR049704	Aminotransferases class-III pyridoxal-phosphate attachment site	Conserved Site
A	IPR050103	Class-III Pyridoxal-phosphate-dependent Aminotransferase	Family
A	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A	IPR017747	Putrescine aminotransferase	Family
A	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A	IPR005814	Aminotransferase class-III	Family
B	IPR000719	Protein kinase domain	Domain
B	IPR044109	cAMP-dependent protein kinase catalytic subunit	Family
B	IPR017441	Protein kinase, ATP binding site	Binding Site
B	IPR000961	AGC-kinase, C-terminal	Domain
B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
B	IPR008271	Serine/threonine-protein kinase, active site	Active Site