4MXW

Structure of heterotrimeric lymphotoxin LTa1b2 bound to lymphotoxin beta receptor LTbR and 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)
B [auth X]	SCOP2B Superfamily	TNF-like	8064727	3000061	SCOP2B (2022-06-29)
E [auth A]	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)
C [auth Y]	TNF	e4mxwY1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
D [auth Z]	TNF	e4mxwZ1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
F [auth B]	TNF	e4mxwB1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
G [auth D]	TNF	e4mxwD1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
I [auth W]	C1-set_1	e4mxwW1	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)
I [auth W]	V-set_10	e4mxwW2	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)
J [auth H]	C1-set_1	e4mxwH1	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)
J [auth H]	V-set_10	e4mxwH2	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)
K [auth V]	C1-set_4	e4mxwV1	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)
K [auth V]	V-set	e4mxwV2	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)
L	C1-set_4	e4mxwL1	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)
L	V-set	e4mxwL2	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)
A [auth S]	TNFR_c6_2	e4mxwS1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_2	ECOD (1.6)
A [auth S]	TNFR_c6_1	e4mxwS2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
H [auth R]	TNFR_c6_2	e4mxwR2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_2	ECOD (1.6)
H [auth R]	TNFR_c6_1	e4mxwR1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)
H [auth R]	TNFR_c6	e4mxwR3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
B [auth X]	TNF	e4mxwX1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
E [auth A]	TNF	e4mxwA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth Y]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D [auth Z]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F [auth B]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
G [auth D]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
I [auth W]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth V]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth S]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
H [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)
B [auth X]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E [auth A]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		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
I [auth W], J [auth H]	anti-Lymphotoxin alpha antibody	VH-CH1	Homo sapiens (human)	IGHV3-7401, IGHV3-7402, IGHV3-7403, IGHJ601, IGHJ602, IGHG101, IGHG102, IGHG104, IGHG1*05	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202432-0)
K [auth V], L	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 (202432-0)
A [auth S], H [auth R]	TNFRSF3 (Tumor necrosis factor receptor superfamily member)	LTBR	Homo sapiens (human)	LTBR*01	R-LIKE-DOMAIN TNFR-CYS	RPI	LTBR	IMGT (202432-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
I [auth W], J [auth H]	Heavy Chain	IGHV3	-	lymphotoxin-alpha	SAbDab (2024-08-16)
K [auth V], L	Light Chain	IGKV1	Kappa	lymphotoxin-alpha	SAbDab (2024-08-16)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
I [auth W], J [auth H]	Pateclizumab	LTA	Therapeutic SAbDab (2024-08-16)
K [auth V], L	Pateclizumab	LTA	Therapeutic SAbDab (2024-08-16)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth Y], D [auth Z], F [auth B], G [auth D]	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain
A [auth S], H [auth R]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region	-	Domain
B [auth X], E [auth A]	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
C [auth Y], D [auth Z], F [auth B], G [auth D]	Lymphotoxin-beta	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	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling biosynthetic process cellular biosynthetic process cellular metabolic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic 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 immune response skin development cell-cell signaling regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death cell surface receptor signaling pathway regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway cell death positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of interleukin-12 production positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process interleukin-12 production regulation of biosynthetic process regulation of cellular metabolic process regulation of macromolecule metabolic process positive regulation of interleukin-12 production regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process	cell periphery plasma membrane membrane cellular anatomical entity extracellular region extracellular space
I [auth W], J [auth H]	anti-Lymphotoxin alpha antibody heavy chain	-	-	-
K [auth V], L	anti-Lymphotoxin alpha antibody light chain	-	-	-
A [auth S], H [auth R]	Tumor necrosis factor receptor superfamily member 3	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process positive regulation of signaling positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell activation cell development mononuclear cell differentiation myeloid leukocyte activation leukocyte activation myeloid cell differentiation cell differentiation myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus immune response apoptotic process cell death programmed cell death regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death cell surface receptor signaling pathway regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane
B [auth X], E [auth A]	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 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 positive regulation of biosynthetic process cytokine production 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth Y], D [auth Z], F [auth B], G [auth D]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
C [auth Y], D [auth Z], F [auth B], G [auth D]	IPR006052	Tumour necrosis factor domain	Domain
C [auth Y], D [auth Z], F [auth B], G [auth D]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
C [auth Y], D [auth Z], F [auth B], G [auth D]	IPR006053	Tumour necrosis factor	Family
C [auth Y], D [auth Z], F [auth B], G [auth D]	IPR002961	Lymphotoxin-beta	Family
A [auth S], H [auth R]	IPR017349	Tumour necrosis factor receptor 3	Family
A [auth S], H [auth R]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A [auth S], H [auth R]	IPR033997	Tumour necrosis factor receptor 3, N-terminal	Domain
B [auth X], E [auth A]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
B [auth X], E [auth A]	IPR006052	Tumour necrosis factor domain	Domain
B [auth X], E [auth A]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
B [auth X], E [auth A]	IPR006053	Tumour necrosis factor	Family
B [auth X], E [auth A]	IPR002960	Lymphotoxin-alpha	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth Y], D [auth Z], F [auth B], G [auth D]	Pharos: Q06643	Liver Cirrhosis, Experimental ulcerative colitis cutaneous lupus erythematosus metabolic syndrome X psoriasis Sjogren syndrome tuberculosis atopic eczema B-cell chronic lymphocytic leukemia Crohn disease glioblastoma interstitial cystitis malignant glioma myositis psoriatic arthritis Liver Cirrhosis, Experimental ulcerative colitis cutaneous lupus erythematosus metabolic syndrome X psoriasis Sjogren syndrome tuberculosis atopic eczema B-cell chronic lymphocytic leukemia Crohn disease glioblastoma interstitial cystitis malignant glioma myositis psoriatic arthritis squamous cell lung carcinoma atypical teratoid rhabdoid tumor cancer Hashimoto thyroiditis large cell medulloblastoma lung adenocarcinoma membranous glomerulonephritis osteosarcoma rheumatoid arthritis Stevens-Johnson syndrome autism spectrum disorder cervical cancer Dengue hemorrhagic fever hypertensive disorder laryngeal squamous cell carcinoma lung carcinoma
A [auth S], H [auth R]	Pharos: P36941	malaria ankylosing spondylitis colorectal cancer psoriasis celiac disease Crohn disease ovarian cancer subependymal giant cell astrocytoma colorectal adenoma juvenile idiopathic arthritis primary biliary cholangitis tuberculosis
B [auth X], E [auth A]	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 Dengue hemorrhagic fever squamous cell lung carcinoma 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 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 R01GM133198.