5XBM | pdb_00005xbm

Structure of SCARB2-JL2 complex

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Chlorophyllase2	e5xbmF1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
C	ACPS	e5xbmC1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: ACPS	ECOD (develop294)
E	Chlorophyllase2	e5xbmE1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)
B	ACPS	e5xbmB1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: ACPS	ECOD (develop294)
A	ACPS	e5xbmA1	A: alpha bundles	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: ACPS	ECOD (develop294)
D	Chlorophyllase2	e5xbmD1	A: alpha bundles	X: PriB N-terminal domain-like	H: gp11/gp12 receptor-binding domain	T: gp11/gp12 receptor-binding domain	F: Chlorophyllase2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	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)

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
B, E	Fab JL2	VH-CH1	Mus musculus (house mouse)	IGHV1-4201, IGHV1-3901, IGHJ202, IGHJ203, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	(VH-CH1)_L-KAPPA	IMGT (202610-0)
A, D	Fab JL2	L-KAPPA	Mus musculus (house mouse)	IGKV5-3901, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	(VH-CH1)_L-KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Heavy Chain	IGHV1	-	lysosome membrane protein 2	SAbDab (2026-03-20)
A, D	Light Chain	IGKV5	Kappa	lysosome membrane protein 2	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F	PF01130	CD36 family (CD36)	CD36 family	The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	Lysosome membrane protein 2	protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cargo receptor activity scavenger receptor activity protein-folding chaperone binding identical protein binding protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cargo receptor activity scavenger receptor activity protein-folding chaperone binding identical protein binding protein homodimerization activity protein dimerization activity cation binding ion binding phosphatidylcholine binding phospholipid binding quaternary ammonium group binding enzyme binding modified amino acid binding anion binding phosphatidylserine binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport sphingolipid catabolic process catabolic process regulation of cellular process glycolipid metabolic process localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport sphingolipid catabolic process catabolic process regulation of cellular process glycolipid metabolic process regulation of lipid metabolic process carbohydrate derivative metabolic process regulation of primary metabolic process regulation of glucosylceramide catabolic process ceramide catabolic process glycosylceramide metabolic process ceramide metabolic process regulation of biological process carbohydrate derivative catabolic process lipid catabolic process glycosphingolipid catabolic process glycosphingolipid metabolic process biological regulation liposaccharide metabolic process primary metabolic process sphingolipid metabolic process glucosylceramide metabolic process regulation of catabolic process regulation of lipid catabolic process glycosylceramide catabolic process glycolipid catabolic process metabolic process cellular process glucosylceramide catabolic process regulation of metabolic process lipid metabolic process regulation of cellular component organization vacuole organization lytic vacuole organization regulation of vacuole organization regulation of organelle organization cellular component organization lysosome organization organelle organization regulation of lysosome organization cellular component organization or biogenesis autophagy process utilizing autophagic mechanism regulation of neuron projection development multicellular organismal process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of carbohydrate catabolic process carbohydrate metabolic process carbohydrate catabolic process regulation of carbohydrate metabolic process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus regulation of endosome organization vesicle organization endosome organization endomembrane system organization cellular localization establishment of protein localization protein targeting establishment of protein localization to vacuole intracellular transport protein localization to vacuole lysosomal transport protein localization to lysosome establishment of protein localization to organelle protein transport protein targeting to lysosome establishment of localization in cell protein localization to organelle vacuolar transport intracellular protein localization protein targeting to vacuole intracellular protein transport establishment of protein localization to plasma membrane vesicle-mediated transport endocytic recycling protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport import into cell receptor-mediated endocytosis endocytosis	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome intracellular vesicle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell periphery plasma membrane endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole membrane lysosomal membrane Golgi membrane Golgi apparatus
B, E	heavy chain of JL2	-	-	-
A, D	light chain of JL2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR002159	CD36 family	Family
C, F	IPR005429	Lysosome membrane protein II	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: Q14108	action myoclonus-renal failure syndrome Unverricht-Lundborg syndrome progressive myoclonus epilepsy malignant ependymoma medulloblastoma obesity disorder ovarian cancer platelet-type bleeding disorder 10 atherosclerosis Down syndrome psoriasis Gaucher disease glioblastoma intellectual disability lung adenocarcinoma action myoclonus-renal failure syndrome Unverricht-Lundborg syndrome progressive myoclonus epilepsy malignant ependymoma medulloblastoma obesity disorder ovarian cancer platelet-type bleeding disorder 10 atherosclerosis Down syndrome psoriasis Gaucher disease glioblastoma intellectual disability lung adenocarcinoma malignant glioma myopathy oligodendroglioma Pick disease adenoma polycystic ovary syndrome atypical teratoid rhabdoid tumor Progressive myoclonus epilepsy 4 type 2 diabetes mellitus epilepsy Gaucher disease type I hereditary spastic paraplegia juvenile dermatomyositis malaria malignant mesothelioma neurodegenerative disease osteosarcoma pilocytic astrocytoma astrocytic tumor primitive neuroectodermal tumor progressive supranuclear palsy inborn carbohydrate metabolic disorder large cell medulloblastoma

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.