6WN4 | pdb_00006wn4

Structural basis for the binding of monoclonal antibody 5D2 to the tryptophan-rich lipid-binding loop in lipoprotein lipase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody 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 [auth L]	C1-set_4	e6wn4L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
F [auth L]	V-set	e6wn4L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B	C1-set_4	e6wn4B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e6wn4B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E [auth H]	V-set_8	e6wn4H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth H]	C1-set_1	e6wn4H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
A	V-set_8	e6wn4A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
A	C1-set_1	e6wn4A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

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 (utative)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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, F [auth L]	Fab 5D2, anti-LPL	L-KAPPA	Mus musculus (house mouse)	IGKV4-6801, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)
A, E [auth H]	Fab 5D2, anti-LPL	VH-CH1	Mus musculus (house mouse)	IGHV1-7101, IGHV1-62-201, IGHJ201, IGHG102	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, F [auth L]	Light Chain	IGKV4	Kappa	lipoprotein lipase peptide	SAbDab (2025-11-28)
A, E [auth H]	Heavy Chain	IGHV1	-	lipoprotein lipase peptide	SAbDab (2025-11-28)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Lipoprotein lipase peptide	triacylglycerol lipase activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity lipase activity protein binding binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding ion binding calcium ion binding triacylglycerol lipase activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity lipase activity protein binding binding heparan sulfate proteoglycan binding proteoglycan binding carbohydrate derivative binding cation binding ion binding calcium ion binding metal ion binding small molecule binding lipoprotein lipase activity signaling receptor binding phospholipase activity apolipoprotein binding lipoprotein particle binding protein-containing complex binding protein-lipid complex binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein homodimerization activity protein dimerization activity phospholipase A1 activity heparin binding glycosaminoglycan binding sulfur compound binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to chemical stimulus response to stimulus response to chemical response to nutrient cellular response to nutrient cellular process regulation of defense response regulation of biological process regulation of response to external stimulus defense response biological regulation cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to chemical stimulus response to stimulus response to chemical response to nutrient cellular response to nutrient cellular process regulation of defense response regulation of biological process regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response chemical homeostasis homeostatic process triglyceride homeostasis acylglycerol homeostasis lipid homeostasis plasma lipoprotein particle organization multicellular organismal process protein-containing complex organization protein-containing complex remodeling protein-lipid complex organization plasma lipoprotein particle remodeling regulation of plasma lipoprotein particle levels cellular component organization triglyceride-rich lipoprotein particle remodeling very-low-density lipoprotein particle remodeling protein-lipid complex remodeling cellular component organization or biogenesis regulation of cellular process interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of interleukin-1 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process chemokine (C-X-C motif) ligand 2 production regulation of chemokine (C-X-C motif) ligand 2 production positive regulation of chemokine (C-X-C motif) ligand 2 production regulation of chemokine production chemokine production positive regulation of chemokine production developmental process fat cell differentiation positive regulation of fat cell differentiation regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of fat cell differentiation diterpenoid metabolic process retinoid metabolic process primary metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process chylomicron remodeling phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process very-low-density lipoprotein particle clearance plasma lipoprotein particle clearance lipoprotein particle mediated signaling signaling response to endogenous stimulus response to lipoprotein particle response to nitrogen compound cell communication cellular response to low-density lipoprotein particle stimulus low-density lipoprotein particle mediated signaling signal transduction cellular response to lipoprotein particle stimulus connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development tissue development regulation of adipose tissue development anatomical structure development interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production regulation of localization lipid storage lipid localization positive regulation of lipid localization localization regulation of lipid storage regulation of lipid localization macromolecule localization nutrient storage positive regulation of lipid storage sterol homeostasis cholesterol homeostasis response to hexose response to monosaccharide response to carbohydrate response to glucose response to oxygen-containing compound macrophage derived foam cell differentiation foam cell differentiation regulation of macrophage derived foam cell differentiation positive regulation of macrophage derived foam cell differentiation fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process cholesterol storage positive regulation of cholesterol storage regulation of cholesterol storage monocarboxylic acid biosynthetic process small molecule biosynthetic process lipid biosynthetic process organic acid biosynthetic process fatty acid biosynthetic process carboxylic acid biosynthetic process neutral lipid metabolic process lipid catabolic process catabolic process neutral lipid catabolic process glycerolipid catabolic process acylglycerol catabolic process triglyceride catabolic process triglyceride metabolic process glycerolipid metabolic process acylglycerol metabolic process biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external biotic stimulus response to biotic stimulus high-density lipoprotein particle remodeling response to lipid response to fatty acid cellular response to oxygen-containing compound cellular response to fatty acid cellular response to lipid regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production	cellular anatomical structure extracellular region extracellular space cell surface cell periphery plasma membrane membrane protein-containing complex catalytic complex plasma lipoprotein particle lipoprotein particle chylomicron protein-lipid complex very-low-density lipoprotein particle cellular anatomical structure extracellular region extracellular space cell surface cell periphery plasma membrane membrane protein-containing complex catalytic complex plasma lipoprotein particle lipoprotein particle chylomicron protein-lipid complex very-low-density lipoprotein particle triglyceride-rich plasma lipoprotein particle
B, F [auth L]	5D2 FAB LIGHT CHAIN	-	-	-
A, E [auth H]	5D2 FAB HEAVY CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR033906	Lipase, N-terminal	Domain
C, D	IPR013818	Lipase	Domain
C, D	IPR016272	Lipase, LIPH-type	Family
C, D	IPR000734	Triacylglycerol lipase family	Family
C, D	IPR001024	PLAT/LH2 domain	Domain
C, D	IPR002330	Lipoprotein lipase	Family
C, D	IPR036392	PLAT/LH2 domain superfamily	Homologous Superfamily
C, D	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P06858	familial lipoprotein lipase deficiency obesity disorder pancreatitis hyperlipoproteinemia type V familial hyperlipidemia cardiomyopathy hepatitis C virus infection familial hypercholesterolemia Hypercholesterolemia malignant colon neoplasm carcinoma hypertensive disorder metabolic syndrome X hypertriglyceridemia prostate cancer familial lipoprotein lipase deficiency obesity disorder pancreatitis hyperlipoproteinemia type V familial hyperlipidemia cardiomyopathy hepatitis C virus infection familial hypercholesterolemia Hypercholesterolemia malignant colon neoplasm carcinoma hypertensive disorder metabolic syndrome X hypertriglyceridemia prostate cancer cardiovascular disease sarcomatoid carcinoma lung carcinoma malignant mesothelioma mammary neoplasms, animal glioblastoma hyperlipidemia atherosclerosis benign colon neoplasm pancreatic intraductal papillary-mucinous neoplasm breast fibroadenoma pilocytic astrocytoma inborn carbohydrate metabolic disorder chronic kidney disease invasive ductal breast carcinoma schizophrenia ulcerative colitis cutaneous lupus erythematosus lung adenocarcinoma ductal breast carcinoma in situ familial apolipoprotein C-II deficiency MALT lymphoma heart disease myocardial infarction hypercholesterolemia, autosomal dominant, type B non-alcoholic fatty liver disease oligodendroglioma atopic eczema breast cancer primitive neuroectodermal tumor inborn errors of metabolism psoriasis colonic neoplasm tuberculosis undifferentiated carcinoma dermatomyositis lung cancer malignant glioma nasopharyngeal carcinoma non-small cell lung carcinoma astrocytic tumor B-cell chronic lymphocytic leukemia hyperlipidemia, familial combined, LPL related osteosarcoma breast carcinoma peripheral arterial disease inherited lipid metabolism disorder Crohn disease type 2 diabetes mellitus

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.