3QCU

Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth H]	d3qcuh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth I]	d3qcui_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d3qcul1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d3qcul2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth M]	d3qcum1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth M]	d3qcum2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], human (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 [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
D [auth M]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	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)
A [auth H]	V-set_8	e3qcuH1	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 [auth H]	C1-set_1	e3qcuH2	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)
C [auth I]	V-set_8	e3qcuI1	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)
C [auth I]	C1-set_1	e3qcuI2	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 L]	C1-set_4	e3qcuL2	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 [auth L]	V-set	e3qcuL1	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 M]	C1-set_4	e3qcuM2	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 M]	V-set	e3qcuM1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth M]	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 [auth H], C [auth I]	LT3015 neutralizing mAb, anti-lysophosphatidic	VH-CH1	Humanized (humanized)	IGHV5-5101, IGHV5-5103, IGHV5-10-104, IGHJ401, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202445-0)
B [auth L], D [auth M]	LT3015 neutralizing mAb, anti-lysophosphatidic	L-KAPPA	Humanized (humanized)	IGKV2D-2902, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202445-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], C [auth I]	Heavy Chain	IGHV5	-	(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL TETRADECANOATE	SAbDab (2024-11-15)
B [auth L], D [auth M]	Light Chain	IGKV2D	Kappa	(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL TETRADECANOATE	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H], C [auth I]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth H], C [auth I]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B [auth L], D [auth M]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H], C [auth I]	LT3015 antibody Fab fragment, heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex
B [auth L], D [auth M]	LT3015 antibody Fab fragment, light chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H], C [auth I]	IPR003597	Immunoglobulin C1-set	Domain
A [auth H], C [auth I]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth H], C [auth I]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth H], C [auth I]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth H], C [auth I]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth H], C [auth I]	IPR007110	Immunoglobulin-like domain	Domain
A [auth H], C [auth I]	IPR050380	Immune Recognition and Response Modulators	Family
A [auth H], C [auth I]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth L], D [auth M]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], D [auth M]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B [auth L], D [auth M]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], D [auth M]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], D [auth M]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], D [auth M]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth L], D [auth M]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency

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.