4MXV

Structure of Lymphotoxin alpha bound to anti-LTa Fab

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family 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)
A	SCOP2B Superfamily	TNF-like	8064727	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8064727	3000061	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	TNF-like	8064727	3000061	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	PF00229	e4mxvA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
B	PF00229	e4mxvB1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
C [auth D]	PF00229	e4mxvD1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
D [auth E]	PF07654	e4mxvE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth E]	PF07686	e4mxvE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth L]	PF07654	e4mxvL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F [auth L]	PF07686	e4mxvL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth X]	PF07654	e4mxvX1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth X]	PF07686	e4mxvX2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth F]	PF07654	e4mxvF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth F]	PF07686	e4mxvF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth H]	PF07654	e4mxvH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth H]	PF07686	e4mxvH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth Y]	PF07654	e4mxvY1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I [auth Y]	PF07686	e4mxvY2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C [auth D]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth Y]	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
D [auth E], F [auth L], H [auth X]	anti-Lymphotoxin alpha antibody	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
E [auth F], G [auth H], I [auth Y]	anti-Lymphotoxin alpha antibody	VH-CH1	Homo sapiens (human)	IGHV3-7401, IGHV3-7402, IGHV3-7403, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth E], F [auth L], H [auth X]	Light Chain	IGKV1	Kappa	lymphotoxin-alpha	SAbDab (2024-04-26)
E [auth F], G [auth H], I [auth Y]	Heavy Chain	IGHV3	-	lymphotoxin-alpha	SAbDab (2024-04-26)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
D [auth E], F [auth L], H [auth X]	Pateclizumab	LTA	Therapeutic SAbDab (2024-04-26)
E [auth F], G [auth H], I [auth Y]	Pateclizumab	LTA	Therapeutic SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D]	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D]	Lymphotoxin-alpha	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	response to stimulus response to chemical response to xenobiotic stimulus 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 humoral immune response response to stimulus response to chemical response to xenobiotic stimulus 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 humoral immune response immune response positive regulation of chronic inflammatory response regulation of defense response chronic inflammatory response regulation of response to external stimulus positive regulation of biological process regulation of chronic inflammatory response to antigenic stimulus inflammatory response to antigenic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response positive regulation of immune response response to stress regulation of response to stress regulation of immune system process positive regulation of chronic inflammatory response to antigenic stimulus positive regulation of immune system process regulation of biological process regulation of chronic inflammatory response defense response regulation of inflammatory response to antigenic stimulus chronic inflammatory response to antigenic stimulus biological regulation response to external stimulus regulation of inflammatory response positive regulation of inflammatory response to antigenic stimulus regulation of response to stimulus positive regulation of defense response regulation of immune response inflammatory response cellular process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of humoral immune response lymphocyte mediated immunity regulation of immune effector process positive regulation of leukocyte mediated immunity regulation of humoral immune response mediated by circulating immunoglobulin positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of B cell mediated immunity humoral immune response mediated by circulating immunoglobulin positive regulation of humoral immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immunoglobulin mediated immune response leukocyte mediated immunity positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immunoglobulin mediated immune response positive regulation of humoral immune response mediated by circulating immunoglobulin regulation of adaptive immune response immunoglobulin mediated immune response adaptive immune response regulation of B cell mediated immunity immune effector process regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity B cell mediated immunity signaling cell-cell signaling cell communication cellular response to stimulus signal transduction negative regulation of cell population proliferation fibroblast proliferation cell population proliferation negative regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of fibroblast proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of nervous system development cellular developmental process regulation of developmental process positive regulation of cell population proliferation cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis regulation of glial cell proliferation gliogenesis positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of cell development nervous system development positive regulation of multicellular organismal process glial cell proliferation response to nutrient levels response to nutrient response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin regulation of type II interferon production type II interferon production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process defense response to Gram-positive bacterium defense response to bacterium defense response to other organism	cell periphery plasma membrane membrane cellular anatomical entity extracellular region extracellular space
D [auth E], F [auth L], H [auth X]	anti-Lymphotoxin alpha antibody light chain	-	-	-
E [auth F], G [auth H], I [auth Y]	anti-Lymphotoxin alpha antibody heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C [auth D]	IPR006052	Tumour necrosis factor domain	Domain
A, B, C [auth D]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
A, B, C [auth D]	IPR006053	Tumour necrosis factor	Family
A, B, C [auth D]	IPR002960	Lymphotoxin-alpha	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C [auth D]	Pharos: P01374	psoriatic arthritis hepatic encephalopathy leprosy malignant mesothelioma myocardial infarction Sepsis coronary artery disease psoriasis Crohn disease esophageal squamous cell carcinoma hepatic coma hypertensive disorder liver disease major depressive disorder metabolic syndrome X psoriatic arthritis hepatic encephalopathy leprosy malignant mesothelioma myocardial infarction Sepsis coronary artery disease psoriasis Crohn disease esophageal squamous cell carcinoma hepatic coma hypertensive disorder liver disease major depressive disorder metabolic syndrome X peripheral nervous system disease AIDS cancer schizophrenia cutaneous lupus erythematosus ulcerative colitis HIV infectious disease laryngeal squamous cell carcinoma lung adenocarcinoma peripheral neuropathy alopecia areata carpal tunnel syndrome squamous cell lung carcinoma Dengue hemorrhagic fever Hashimoto thyroiditis Hodgkins lymphoma lung carcinoma membranous glomerulonephritis myositis autism spectrum disorder rheumatoid arthritis cervical cancer Stevens-Johnson syndrome herpes zoster

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.