3ZKM | pdb_00003zkm

BACE2 FAB COMPLEX

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth L]	d3zkml2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	HUMAN (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F [auth L]	d3zkml1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3zkmd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	HUMAN (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3zkmd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	HUMAN (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E [auth H]	d3zkmh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3zkmc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3zkmb_	All beta proteins	Acid proteases	Acid proteases	automated matches	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3zkma_	All beta proteins	Acid proteases	Acid proteases	automated matches	automated matches	(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)
B	SCOP2B Superfamily	Acid proteases	8066379	3001059	SCOP2B (2022-06-29)
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)
F [auth L]	Peptidase_M10	e3zkmL1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: Peptidase_M10	ECOD (v294.1)
D	Globin	e3zkmD1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: Globin	ECOD (v294.1)
E [auth H]	PGM_PMM_IV	e3zkmH1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: PGM_PMM_IV	ECOD (v294.1)
C	Globin	e3zkmC1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: Globin	ECOD (v294.1)
B	Vinculin	e3zkmB2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (v294.1)
A	Vinculin	e3zkmA2	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
D, F [auth L]	FAB-GAMMA-2A_KAPPA	V-KAPPA	Mus musculus (house mouse)	IGKV3-1001, IGKJ101	V-DOMAIN V-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202613-0)
C, E [auth H]	FAB-GAMMA-2A_KAPPA	VH-CH1	Mus musculus (house mouse)	IGHV2-902, IGHJ401, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D, F [auth L]	Light Chain	IGKV3	Kappa	beta-secretase 2	SAbDab (2026-04-10)
C, E [auth H]	Heavy Chain	IGHV2	-	beta-secretase 2	SAbDab (2026-04-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
D, F [auth L]	FAB LIGHT CHAIN	-	-	-
C, E [auth H]	FAB HEAVY CHAIN	-	-	-
A, B	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 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 amyloid-beta metabolic process metabolic process cellular 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

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, E [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.