1ZVO

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
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)
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)
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)
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)

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, 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 (202414-0)
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 (202414-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, B	Light Chain	IGLV1	Lambda	-	SAbDab (2024-04-12)
C, D	Heavy Chain	IGHV4	-	-	SAbDab (2024-04-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
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	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
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-prot ...	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	myeloma immunoglobulin D lambda	binding antigen binding	response to stimulus immune response immune system process adaptive immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling response to stimulus immune response immune system process adaptive immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process 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 B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	extracellular region extracellular space cellular anatomical entity blood microparticle cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex IgA immunoglobulin complex IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome extracellular region extracellular space cellular anatomical entity blood microparticle cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex IgA immunoglobulin complex IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle IgG immunoglobulin complex
C, D	Immunoglobulin delta heavy chain	-	multicellular organismal process regulation of cellular process interleukin-1 production cellular biosynthetic process positive regulation of biological 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 regulation of cytokine production organic substance biosynthetic process cytokine production positive regulation of interleukin-1 production multicellular organismal process regulation of cellular process interleukin-1 production cellular biosynthetic process positive regulation of biological 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 regulation of cytokine production organic substance biosynthetic process 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 cellular metabolic process biological regulation 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 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 positive regulation of cellular biosynthetic process monocyte activation immune system process cell activation myeloid leukocyte activation leukocyte activation response to stimulus immune response adaptive immune response regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production regulation of interleukin-1 beta production positive regulation of interleukin-1 beta production interleukin-1 beta production	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR003599	Immunoglobulin subtype	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
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
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR003599	Immunoglobulin subtype	Domain
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	IPR013106	Immunoglobulin V-set domain	Domain
C, D	IPR013151	Immunoglobulin	Domain
C, D	IPR007110	Immunoglobulin-like domain	Domain
C, D	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P01700	B-cell chronic lymphocytic leukemia malignant pancreatic neoplasm pancreatic ductal adenocarcinoma periodontitis ulcerative colitis cystic fibrosis non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma sinusitis interstitial cystitis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm tuberculosis

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.