2AGJ

Crystal Structure of a glycosylated Fab from an IgM cryoglobulin with properties of a natural proteolytic antibody

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
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d2agjl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d2agjl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d2agjh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d2agjh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain mu constant domain 1, CH1-mu	(Homo sapiens ) [TaxId: 9606 ],	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 [auth L]	C1-set_4	e2agjL2	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 [auth L]	V-set	e2agjL1	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 [auth H]	V-set_8	e2agjH1	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 [auth H]	C1-set_1	e2agjH2	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 [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	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 L]	Yvo	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-MU_KAPPA	IMGT (202415-0)
B [auth H]	Yvo	VH-CH1	Homo sapiens (human)	IGHV2-501, IGHV2-509, IGHJ401, IGHJ402, IGHJ403, IGHM03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-MU_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV3	Kappa	-	SAbDab (2024-04-19)
B [auth H]	Heavy Chain	IGHV2	-	-	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth L]	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 L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B [auth H]	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 L]	Yvo Fab, Light Chain	-	-	extracellular region cellular anatomical entity
B [auth H]	Yvo Fab, Heavy Chain	binding antigen binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus 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 cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus 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 immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin leukocyte mediated immunity complement activation, classical pathway immunoglobulin mediated immune response immune effector process B cell mediated immunity biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus antibacterial humoral response defense response to symbiont antimicrobial humoral response innate immune response multicellular organismal process cellular developmental process immature B cell differentiation cellular biosynthetic process cell development mononuclear cell differentiation pre-B cell allelic exclusion pre-B cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation organic substance metabolic process cell differentiation anatomical structure development organic substance biosynthetic process developmental process regulation of biosynthetic process hemopoiesis B cell activation cellular metabolic process cell activation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process leukocyte differentiation	hexameric IgM immunoglobulin complex protein-containing complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space cellular anatomical entity immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex hexameric IgM immunoglobulin complex protein-containing complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space cellular anatomical entity immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex membrane protein complex receptor complex B cell receptor complex cell periphery plasma membrane signaling receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle pentameric IgM immunoglobulin complex cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L]	IPR003599	Immunoglobulin subtype	Domain
A [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth H]	Pharos: P01871	autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm sinusitis ulcerative colitis autosomal agammaglobulinemia Bruton-type agammaglobulinemia Hypogammaglobulinemia lung cancer malignant pancreatic neoplasm osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.