3IET

Crystal Structure of 237mAb with antigen

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ieta1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3ieta2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3ietc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3ietc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	C1-set_4	e3ietA2	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)
A	V-set	e3ietA1	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)
C	C1-set_4	e3ietC2	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)
C	V-set	e3ietC1	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	V-set_8	e3ietB1	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	C1-set_1	e3ietB2	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)
D	V-set_8	e3ietD1	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)
D	C1-set_1	e3ietD2	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)
A	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	2.60.40.10	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
A, C	237 mAb	L-KAPPA	Mus musculus (house mouse)	IGKV1-11001, IGKJ101, IGKJ102, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202415-0)
B, D	237 mAb	VH-CH1	Mus musculus (house mouse)	IGHV6-601, IGHJ201, IGHJ401, IGHG2A01, IGHG2A*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, C	Light Chain	IGKV1	Kappa	podoplanin	SAbDab (2024-04-19)
B, D	Heavy Chain	IGHV6	-	podoplanin	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth X], F [auth Q]	PF05808	Podoplanin (Podoplanin)	Podoplanin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Immunoglobulin light chain (IgG2a)	-	-	-
B, D	Immunoglobulin heavy chain (IgG2a)	-	-	-
E [auth X], F [auth Q]	Podoplanin	protein binding binding chemokine binding cytokine binding protein-folding chaperone binding signaling receptor binding	regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development regulation of biological process cell adhesion regulation of cellular process regulation of cell adhesion biological regulation cellular process developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development anatomical structure morphogenesis tube morphogenesis tube development regulation of actin filament-based process actin filament-based movement regulation of actin filament-based movement regulation of myofibroblast contraction actin filament-based process myofibroblast contraction actin-mediated cell contraction cell population proliferation regulation of cell-substrate adhesion regulation of substrate adhesion-dependent cell spreading substrate adhesion-dependent cell spreading cell-substrate adhesion prostaglandin metabolic process icosanoid metabolic process fatty acid metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process prostanoid metabolic process organic substance metabolic process cellular lipid metabolic process small molecule metabolic process metabolic process monocarboxylic acid metabolic process lipid metabolic process cell migration cell motility regulation of body fluid levels response to stimulus homotypic cell-cell adhesion positive regulation of biological process regulation of cell activation positive regulation of cell-cell adhesion cell-cell adhesion response to stress coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of biological quality response to wounding positive regulation of cellular process wound healing regulation of homotypic cell-cell adhesion positive regulation of cell adhesion cell activation hemostasis platelet aggregation blood coagulation regulation of platelet activation regulation of platelet aggregation positive regulation of homotypic cell-cell adhesion positive regulation of platelet aggregation platelet activation positive regulation of locomotion regulation of cell motility regulation of locomotion positive regulation of cell motility locomotion cellular response to stimulus small GTPase-mediated signal transduction signaling Rho protein signal transduction intracellular signal transduction cell communication intracellular signaling cassette signal transduction cellular component disassembly extracellular matrix disassembly regulation of cellular component organization positive regulation of cellular component organization positive regulation of extracellular matrix organization extracellular matrix organization positive regulation of extracellular matrix disassembly cellular component organization cellular component organization or biogenesis regulation of extracellular matrix organization regulation of extracellular matrix disassembly extracellular structure organization external encapsulating structure organization heart development epithelium development visceral serous pericardium development tissue development circulatory system development pericardium development negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of epithelial to mesenchymal transition regulation of developmental process cellular developmental process positive regulation of epithelial to mesenchymal transition regulation of cell differentiation mesenchyme development positive regulation of developmental process positive regulation of cell differentiation cell differentiation epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation lymphangiogenesis vasculature development anatomical structure formation involved in morphogenesis lymph vessel morphogenesis lymph vessel development respiratory tube development lung development respiratory system development cell projection organization plasma membrane bounded cell projection morphogenesis cell morphogenesis regulation of cell morphogenesis cell projection morphogenesis regulation of lamellipodium organization regulation of lamellipodium morphogenesis regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization lamellipodium organization lamellipodium morphogenesis regulation of plasma membrane bounded cell projection organization regulation of cell shape negative regulation of cell population proliferation regulation of cell population proliferation positive regulation of cell migration regulation of cell migration positive regulation of platelet activation positive regulation of cell activation endothelial cell fate commitment endothelial cell differentiation endothelium development epithelial cell fate commitment lymphatic endothelial cell differentiation epithelial cell differentiation lymphatic endothelial cell fate commitment cell fate commitment regulation of cell cycle phase transition regulation of cell cycle process cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle regulation of mitotic cell cycle phase transition regulation of mitotic cell cycle regulation of G1/S transition of mitotic cell cycle mitotic cell cycle process cell cycle regulation of cell cycle G1/S transition of mitotic cell cycle cell cycle process mitotic cell cycle phase transition morphogenesis of an epithelium epiboly involved in wound healing morphogenesis of an epithelial sheet tissue morphogenesis epiboly wound healing, spreading of cells lung alveolus development response to oxygen levels response to abiotic stimulus response to hyperoxia response to increased oxygen levels	cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol cell projection cell leading edge cellular anatomical entity plasma membrane bounded cell projection lamellipodium cell periphery cell surface membrane plasma membrane external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm cytosol actin-based cell projection plasma membrane region microvillus microvillus membrane cell projection membrane basal part of cell basal plasma membrane basolateral plasma membrane ruffle filopodium membrane-bounded organelle intracellular organelle mitochondrion organelle intracellular membrane-bounded organelle cell junction apical part of cell apical plasma membrane leading edge membrane ruffle membrane anchoring junction leading edge of lamellipodium membrane microdomain membrane raft lamellipodium membrane cytoplasmic vesicle intracellular vesicle vesicle tetraspanin-enriched microdomain filopodium membrane

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.