3N56 | pdb_00003n56

Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Phospholip_A2_1	e3n56A1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
A	PRDM2_PR	e3n56A11	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: PRDM2_PR	ECOD (develop294)
B	Phospholip_A2_1	e3n56B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
B	PRDM2_PR	e3n56B11	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: PRDM2_PR	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)
B	3.30.830.10	Alpha Beta	2-Layer Sandwich	Cytochrome Bc1 Complex	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05193	Peptidase M16 inactive domain (Peptidase_M16_C)	Peptidase M16 inactive domain	Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp [1].	Domain
A, B	PF16187	Middle or third domain of peptidase_M16 (Peptidase_M16_M)	Middle or third domain of peptidase_M16	-	Family
A, B	PF00675	Insulinase (Peptidase family M16) (Peptidase_M16)	Insulinase (Peptidase family M16)	-	Family
C, D	PF00212	Atrial natriuretic peptide (ANP)	Atrial natriuretic peptide	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Insulin-degrading enzyme	amyloid-beta binding binding peptide binding protein binding peptide hormone binding hormone binding insulin binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding amyloid-beta binding binding peptide binding protein binding peptide hormone binding hormone binding insulin binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein-containing complex binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity beta-endorphin binding identical protein binding virus receptor activity exogenous protein binding metalloendopeptidase activity metallopeptidase activity protein homodimerization activity protein dimerization activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding	catabolic process metabolic process cellular process peptide metabolic process peptide catabolic process multicellular organismal process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic process amyloid-beta clearance primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process catabolic process metabolic process cellular process peptide metabolic process peptide catabolic process multicellular organismal process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic process amyloid-beta clearance primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process cellular homeostasis homeostatic process ubiquitin recycling bradykinin catabolic process cellular respiration aerobic respiration regulation of biological process regulation of cellular process energy derivation by oxidation of organic compounds biological regulation regulation of generation of precursor metabolites and energy generation of precursor metabolites and energy regulation of cellular respiration regulation of aerobic respiration regulation of metabolic process regulation of protein binding positive regulation of molecular function regulation of molecular function positive regulation of protein binding regulation of binding positive regulation of binding insulin metabolic process positive regulation of protein metabolic process positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of protein metabolic process regulation of macromolecule metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process negative regulation of proteolysis negative regulation of metabolic process negative regulation of biological process regulation of proteolysis proteolysis negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process cellular response to stimulus cellular response to nitrogen compound response to stimulus signaling response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular response to endogenous stimulus response to hormone signal transduction enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus cell surface receptor signaling pathway response to endogenous stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin cellular response to insulin stimulus antigen processing and presentation immune system process antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I regulation of hormone levels regulation of biological quality hormone metabolic process hormone catabolic process insulin catabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex catalytic complex peptidase complex cytosolic proteasome complex proteasome complex endopeptidase complex intracellular protein-containing complex intracellular organelle peroxisome microbody intracellular membrane-bounded organelle peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen mitochondrion nucleus
C, D	Natriuretic peptides B	protein binding binding signaling receptor binding hormone receptor binding hormone activity diuretic hormone activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway multicellular organismal process system process circulatory system process cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway multicellular organismal process system process circulatory system process regulation of blood pressure regulation of biological quality blood circulation protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation regulation of body fluid levels renal system process positive regulation of urine volume regulation of urine volume regulation of vascular permeability vascular process in circulatory system regulation of growth regulation of cellular component organization negative regulation of biological process growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth negative regulation of cellular process cellular component organization or biogenesis body fluid secretion localization secretion transport establishment of localization regulation of tube diameter regulation of tube size blood vessel diameter maintenance vasodilation regulation of anatomical structure size cell surface receptor signaling pathway regulation of localization renal sodium excretion inorganic ion homeostasis regulation of renal system process homeostatic process regulation of system process positive regulation of biological process positive regulation of secretion monoatomic ion homeostasis regulation of multicellular organismal process monoatomic cation homeostasis positive regulation of renal sodium excretion excretion sodium ion homeostasis regulation of transport renal tubular secretion regulation of secretion regulation of renal sodium excretion positive regulation of transport chemical homeostasis positive regulation of multicellular organismal process regulation of excretion developmental process heart development cardiac conduction system development cardiac muscle tissue development animal organ development tissue development striated muscle tissue development circulatory system development multicellular organism development anatomical structure development muscle tissue development system development regulation of systemic arterial blood pressure negative regulation of systemic arterial blood pressure negative regulation of blood pressure ribose phosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process cyclic nucleotide metabolic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process cyclic nucleotide biosynthetic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cyclic purine nucleotide metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process cGMP metabolic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process purine ribonucleotide metabolic process cGMP biosynthetic process purine nucleotide biosynthetic process regulation of developmental process angiogenesis regulation of vasculature development tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development negative regulation of vasculature development anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process receptor guanylyl cyclase signaling pathway enzyme-linked receptor protein signaling pathway	cellular anatomical structure intracellular anatomical structure cytoplasm protein-containing complex extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011249	Metalloenzyme, LuxS/M16 peptidase-like	Homologous Superfamily
A, B	IPR001431	Peptidase M16, zinc-binding site	Binding Site
A, B	IPR007863	Peptidase M16, C-terminal	Domain
A, B	IPR054734	Coenzyme PQQ synthesis protein F-like, C-terminal lobe, domain 4	Domain
A, B	IPR011765	Peptidase M16, N-terminal	Domain
A, B	IPR050626	Peptidase M16	Family
A, B	IPR032632	Peptidase M16, middle/third domain	Domain
C, D	IPR030480	Natriuretic peptide, conserved site	Conserved Site
C, D	IPR002408	Natriuretic peptide, brain type	Family
C, D	IPR050787	Natriuretic Peptide Hormone	Family
C, D	IPR000663	Natriuretic peptide	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P14735	Alzheimer disease Presenile dementia atopic eczema large cell medulloblastoma malignant ependymoma osteosarcoma psoriasis atypical teratoid rhabdoid tumor glioblastoma lung cancer non-alcoholic fatty liver disease ovarian cancer schizophrenia amyotrophic lateral sclerosis dementia Alzheimer disease Presenile dementia atopic eczema large cell medulloblastoma malignant ependymoma osteosarcoma psoriasis atypical teratoid rhabdoid tumor glioblastoma lung cancer non-alcoholic fatty liver disease ovarian cancer schizophrenia amyotrophic lateral sclerosis dementia invasive ductal breast carcinoma lymphoplasmacytic lymphoma non-small cell lung carcinoma
C, D	Pharos: P16860	hypertensive disorder atrial fibrillation sickle cell anemia dilated cardiomyopathy heart disease aortic valve insufficiency coronary artery disease cardiomyopathy Ventricular Dysfunction, Left pulmonary hypertension cardiovascular disease potassium deficiency disease ureteral obstruction ventricular tachycardia congestive heart failure hypertensive disorder atrial fibrillation sickle cell anemia dilated cardiomyopathy heart disease aortic valve insufficiency coronary artery disease cardiomyopathy Ventricular Dysfunction, Left pulmonary hypertension cardiovascular disease potassium deficiency disease ureteral obstruction ventricular tachycardia congestive heart failure psoriasis cystic fibrosis kidney failure hypotensive disorder pericardial effusion congenital heart disease dilated cardiomyopathy 1A familial atrial fibrillation heart failure inborn carbohydrate metabolic disorder brain injury intracerebral hemorrhage

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.