1ZVO | pdb_00001zvo

Semi-extended solution structure of human myeloma immunoglobulin D determined by constrained X-ray scattering

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
B	d1zvob1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain lambda variable domain, VL-lambda	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1zvob2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain lambda constant domain, CL-lambda	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1zvoa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain lambda variable domain, VL-lambda	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1zvoa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain lambda constant domain, CL-lambda	(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)
D	C1-set	e1zvoD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
D	C1-set_1	e1zvoD1	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)
D	V-set_12	e1zvoD4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
D	EUF08782	e1zvoD5	A: extended segments	X: Myeloma immunoglobulin D delta linker region (From Topology)	H: Myeloma immunoglobulin D delta linker region (From Topology)	T: Myeloma immunoglobulin D delta linker region	F: EUF08782	ECOD (1.6)
C	C1-set	e1zvoC4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
C	C1-set_1	e1zvoC2	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	V-set_12	e1zvoC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C	EUF08782	e1zvoC3	A: extended segments	X: Myeloma immunoglobulin D delta linker region (From Topology)	H: Myeloma immunoglobulin D delta linker region (From Topology)	T: Myeloma immunoglobulin D delta linker region	F: EUF08782	ECOD (1.6)
B	C1-set	e1zvoB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
B	V-set_3	e1zvoB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
A	C1-set	e1zvoA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
A	V-set_3	e1zvoA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)

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
C, D	WAH (human myeloma IgD) IGLC2 G1.5>S	H-DELTA	Homo sapiens (human)	IGHV4-3901, IGHV4-3906, IGHV4-3907, IGHJ601, IGHJ602, IGHD01, IGHD*02	V-DOMAIN VH, C-DOMAIN CH1, C-DOMAIN CH2, C-DOMAIN CH3	IG	IG-DELTA_LAMBDA	IMGT (202540-0)
A, B	WAH (human myeloma IgD) IGLC2 G1.5>S	L-LAMBDA	Homo sapiens (human)	IGLV1-4701, IGLV1-4702, IGLJ302, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	IG-DELTA_LAMBDA	IMGT (202540-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV4	-	-	SAbDab (2025-10-17)
A, B	Light Chain	IGLV1	Lambda	-	SAbDab (2025-10-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF20838	Immunoglobulin D, delta linker region (IgD_del_linker)	Immunoglobulin D, delta linker region	The linker region of Immunoglobulin D (IgD), the longest hinge sequence of any immunoglobulin, connects the Fab and Fc fragments. It has up to seven O-linked oligosaccharide sites, which is thought to be related to the flexible T-shape of IgD [1].	Domain
C, D	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, D	PF00047	Immunoglobulin domain (ig)	Immunoglobulin domain	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-prote ...	Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.	Domain
A, B	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
C, D	Immunoglobulin delta heavy chain	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process multicellular organismal process regulation of cellular process interleukin-1 production positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production positive regulation of interleukin-1 production regulation of multicellular organismal process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of interleukin-1 production biological regulation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway response to stimulus signaling 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 cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway regulation of response to stimulus immune system process regulation of immune response 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 antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	cellular anatomical structure extracellular region extracellular space blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle cellular anatomical structure extracellular region extracellular space blood microparticle protein-containing complex immunoglobulin complex, circulating 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
A, B	myeloma immunoglobulin D lambda	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 anatomical structure extracellular region extracellular space blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane cellular anatomical structure extracellular region extracellular space blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR013151	Immunoglobulin-like beta-sandwich domain	Domain
C, D	IPR050380	Immune Recognition and Response Modulators	Family
C, D	IPR049351	Immunoglobulin delta heavy chain-like, delta linker region	Domain
C, D	IPR003597	Immunoglobulin C1-set	Domain
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR007110	Immunoglobulin-like domain	Domain
C, D	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A, B	IPR003597	Immunoglobulin C1-set	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P01880	B-cell chronic lymphocytic leukemia gastric carcinoma nasopharyngeal carcinoma psoriasis exocrine pancreatic carcinoma lung cancer osteosarcoma tuberculosis gastric cancer malignant pancreatic neoplasm plasma cell myeloma ulcerative colitis

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.