7SGM

Crystal structure of a Fab variant containing a fluorescent noncanonical amino acid with blocked excited state proton transfer and in complex with its antigen, CD40L

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	8041217	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8041217	3000061	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TNF-like	8041217	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	e7sgmA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
B	PF00229	e7sgmB1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
C	PF00229	e7sgmC1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
D [auth H]	PF07654	e7sgmH2	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 H]	PF07686	e7sgmH1	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 K]	PF07654	e7sgmK1	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 K]	PF07686	e7sgmK2	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	e7sgmX2	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	e7sgmX1	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 L]	PF07654	e7sgmL1	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 L]	PF07686	e7sgmL2	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 M]	PF07654	e7sgmM2	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 M]	PF07686	e7sgmM1	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	e7sgmY2	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	e7sgmY1	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)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
D [auth H], F [auth K], H [auth X]	Tegoprubart	CD40LG/CD154	Therapeutic SAbDab (2024-05-10)
E [auth L], G [auth M], I [auth Y]	Ruplizumab	CD40LG/CD154	Therapeutic SAbDab (2024-05-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	CD40 ligand	protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding CD40 receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity protein binding binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding CD40 receptor binding cell adhesion molecule binding protein-containing complex binding integrin binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity tumor necrosis factor receptor binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation 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 cellular response to stimulus integrin-mediated signaling pathway cell surface receptor signaling pathway response to stimulus signaling cell communication signal transduction cellular biosynthetic process positive regulation of biological process regulation of interleukin-12 production 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 regulation of multicellular organismal process positive regulation of macromolecule metabolic process interleukin-12 production positive regulation of cellular 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 interleukin-12 production regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process 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 CD40 signaling pathway regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation cell population proliferation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process regulation of DNA-templated transcription regulation of immune effector process immunoglobulin production regulation of immune system process production of molecular mediator of immune response immune effector process regulation of immunoglobulin production regulation of production of molecular mediator of immune response interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production positive regulation of epithelial cell apoptotic process positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death regulation of epithelial cell apoptotic process positive regulation of apoptotic process epithelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process cell adhesion cell-cell adhesion leukocyte cell-cell adhesion regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation T cell activation positive regulation of leukocyte activation regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion T cell costimulation regulation of lymphocyte activation defense response inflammatory response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell activation involved in immune response cell activation involved in immune response multicellular organism development leukocyte mediated immunity somatic diversification of immune receptors somatic recombination of immunoglobulin genes involved in immune response system development immune response DNA recombination DNA metabolic process somatic diversification of immunoglobulins B cell mediated immunity isotype switching immune system development immunoglobulin production involved in immunoglobulin-mediated immune response somatic cell DNA recombination somatic diversification of immunoglobulins involved in immune response somatic recombination of immunoglobulin gene segments leukocyte activation involved in immune response lymphocyte activation involved in immune response immunoglobulin mediated immune response adaptive immune response somatic diversification of immune receptors via germline recombination within a single locus regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of cell population proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation T cell proliferation regulation of lymphocyte proliferation regulation of T cell proliferation regulation of mononuclear cell proliferation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system extracellular region extracellular space
D [auth H], F [auth K], H [auth X]	5c8* Fab heavy chain	-	-	-
E [auth L], G [auth M], I [auth Y]	5c8* Fab light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C	IPR006052	Tumour necrosis factor domain	Domain
A, B, C	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
A, B, C	IPR003263	CD40 ligand	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P29965	hyper-IgM syndrome type 1 amyotrophic lateral sclerosis autoimmune disease allergic disease Chromosome Breakage coronary artery disease pulmonary hypertension pneumonia pneumonitis hyper-IgM syndrome X-linked acrogigantism due to Xq26 microduplication cancer hematologic disease lymphatic system disease

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.