6WJL | pdb_00006wjl

Crystal structure of Glypican-2 core protein in complex with D3 Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody 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)
E	SCOP2B Superfamily	Frizzled domain-like	8102915	3001950	SCOP2B (2022-06-29)
A [auth G]	SCOP2 Family	Glypican-like	8102914	4006165	SCOP2 (2022-06-29)
A [auth G]	SCOP2 Superfamily	Frizzled domain-like	8102915	3001950	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H [auth J]	C1-set_4	e6wjlJ2	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)
H [auth J]	V-set	e6wjlJ1	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)
D [auth L]	C1-set_4	e6wjlL1	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)
D [auth L]	V-set	e6wjlL2	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)
G [auth I]	V-set_10	e6wjlI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
C [auth K]	V-set_12	e6wjlK1	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)
F	V-set_8	e6wjlF1	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)
F	C1-set_1	e6wjlF2	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)
B [auth H]	V-set_8	e6wjlH2	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)
B [auth H]	C1-set_1	e6wjlH1	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)
E	Glypican_1st	e6wjlE2	A: alpha complex topology	X: Glypican insertion domain (From Topology)	H: Glypican insertion domain (From Topology)	T: Glypican insertion domain	F: Glypican_1st	ECOD (1.6)
E	Glypican_2nd	e6wjlE1	A: few secondary structure elements	X: Frizzled cysteine-rich domain-related (From Topology)	H: Frizzled cysteine-rich domain-related (From Topology)	T: Frizzled cysteine-rich domain-related	F: Glypican_2nd	ECOD (1.6)
A [auth G]	Glypican_1st	e6wjlG1	A: alpha complex topology	X: Glypican insertion domain (From Topology)	H: Glypican insertion domain (From Topology)	T: Glypican insertion domain	F: Glypican_1st	ECOD (1.6)
A [auth G]	Glypican_2nd	e6wjlG2	A: few secondary structure elements	X: Frizzled cysteine-rich domain-related (From Topology)	H: Frizzled cysteine-rich domain-related (From Topology)	T: Frizzled cysteine-rich domain-related	F: Glypican_2nd	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L], H [auth J]	Light Chain	IGKV1	Kappa	glypican-2	SAbDab (2025-12-26)
B [auth H], F	Heavy Chain	IGHV3	-	glypican-2	SAbDab (2025-12-26)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L], H [auth J]	D3 Fab Light Chain	-	-	-
C [auth K], G [auth I]	VHH domain	-	-	-
B [auth H], F	D3 Fab Heavy chain	-	-	-
A [auth G], E	Glypican-2	-	regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development regulation of neuron projection development multicellular organismal process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development cellular component organization neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization cellular component organization or biogenesis positive regulation of cellular process system development developmental process regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation nervous system development generation of neurons neuron development cellular process regulation of plasma membrane bounded cell projection organization cellular response to stimulus cell surface receptor signaling pathway response to stimulus signaling smoothened signaling pathway cell communication signal transduction regulation of localization cellular localization regulation of protein localization localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization intracellular protein localization regulation of protein localization to membrane regulation of signaling regulation of signal transduction regulation of response to stimulus regulation of cell communication cell migration cell motility	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane side of membrane extracellular region lytic vacuole vacuolar lumen vacuole lysosomal lumen lysosome synapse cell junction cell surface cell periphery plasma membrane endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth G], E	IPR001863	Glypican	Family
A [auth G], E	IPR019803	Glypican, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth G], E	Pharos: Q8N158	large cell medulloblastoma osteosarcoma spina bifida Malignant neoplasm of breast primitive neuroectodermal tumor medulloblastoma psoriasis

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.