6JSZ | pdb_00006jsz

BACE2 xaperone complex with N-{3-[(5R)-3-amino-5-methyl-9,9-dioxo-2,9lambda6-dithia-4-azaspiro[5.5]undec-3-en-5-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Acid proteases	8066379	3001059	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	Asp_C_1	e6jszA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_C_1	ECOD (1.6)
A	Asp_N	e6jszA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Asp_N	ECOD (1.6)
B [auth D]	V-set_12	e6jszD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth D]	Heavy Chain	IGHV3	-	beta-secretase 2	SAbDab (2025-11-07)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00026	Eukaryotic aspartyl protease (Asp)	Eukaryotic aspartyl protease	Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller a ...	Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (Pfam:PF00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Beta-secretase 2	aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity	amyloid-beta metabolic process metabolic process cellular process amide metabolic process vesicle organization cellular component organization melanosome organization organelle organization pigmentation cellular pigmentation cellular component organization or biogenesis pigment granule organization regulation of cellular process negative regulation of biological process amyloid-beta metabolic process metabolic process cellular process amide metabolic process vesicle organization cellular component organization melanosome organization organelle organization pigmentation cellular pigmentation cellular component organization or biogenesis pigment granule organization regulation of cellular process negative regulation of biological process carbohydrate derivative metabolic process regulation of primary metabolic process amyloid precursor protein biosynthetic process negative regulation of cellular process negative regulation of amyloid precursor protein biosynthetic process regulation of amyloid precursor protein biosynthetic process protein metabolic process amyloid precursor protein metabolic process regulation of glycoprotein biosynthetic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process carbohydrate derivative biosynthetic process regulation of biosynthetic process negative regulation of glycoprotein biosynthetic process negative regulation of glycoprotein metabolic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation glycoprotein biosynthetic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process macromolecule biosynthetic process regulation of glycoprotein metabolic process biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process peptide hormone processing regulation of hormone levels signaling receptor ligand precursor processing gene expression hormone metabolic process protein maturation proteolysis protein processing regulation of biological quality chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis membrane protein proteolysis membrane protein ectodomain proteolysis	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm endosome cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus subcompartment Golgi apparatus organelle subcompartment intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle trans-Golgi network cytoplasm endosome intracellular vesicle cytoplasmic vesicle vesicle cell periphery plasma membrane pigment granule chitosome melanosome cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane melanosome membrane organelle membrane pigment granule membrane endoplasmic reticulum
B [auth D]	XAPERONE	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001461	Aspartic peptidase A1	Family
A	IPR009121	Beta-secretase BACE2	Family
A	IPR033121	Peptidase family A1 domain	Domain
A	IPR033874	Memapsin-like	Domain
A	IPR009119	Beta-secretase BACE	Family
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR001969	Aspartic peptidase, active site	Active Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y5Z0	pancreatic intraductal papillary-mucinous neoplasm spina bifida adrenoleukodystrophy cystic fibrosis interstitial cystitis malignant ependymoma malignant pancreatic neoplasm nasopharyngeal carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma Crohn disease Down syndrome large cell medulloblastoma malignant glioma pancreatic intraductal papillary-mucinous neoplasm spina bifida adrenoleukodystrophy cystic fibrosis interstitial cystitis malignant ependymoma malignant pancreatic neoplasm nasopharyngeal carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia subependymal giant cell astrocytoma Crohn disease Down syndrome large cell medulloblastoma malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer ulcerative colitis cutaneous melanoma glioblastoma lung adenocarcinoma malignant mesothelioma melanoma 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.