5IMK | pdb_00005imk

Nanobody targeting human Vsig4 in Spacegroup C2

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth B]	V-set_8	e5imkB1	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 A]	V-set_9	e5imkA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_9	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth A]	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 B]	nAb	VH	Vicugna pacos (alpaca)	IGHV3-301, IGHJ401	V-DOMAIN VH	RPI	1V-1C-LIKE_VH	IMGT (202514-0)
B [auth A]	VSIG4, V-set and immunoglobulin domain-containing protein 4	1V-1C-LIKE	Homo sapiens (human)	VSIG4*01	V-LIKE-DOMAIN V-LIKE, C-LIKE-DOMAIN C-LIKE	RPI	VSIG4	IMGT (202514-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth B]	Heavy Chain	IGHV1	-	v-set and immunoglobulin domain-containing protein 4	SAbDab (2025-04-18)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Nanobody	-	-	-
B [auth A]	V-set and immunoglobulin domain-containing protein 4	opsonin binding protein binding binding complement component C3b binding complement binding	regulation of humoral immune response regulation of immune effector process response to stimulus negative regulation of biological process complement activation, alternative pathway response to biotic stimulus complement activation positive regulation of immune response regulation of immune system process positive regulation of immune system process regulation of biological process regulation of complement activation, alternative pathway immune response response to other organism regulation of humoral immune response regulation of immune effector process response to stimulus negative regulation of biological process complement activation, alternative pathway response to biotic stimulus complement activation positive regulation of immune response regulation of immune system process positive regulation of immune system process regulation of biological process regulation of complement activation, alternative pathway immune response response to other organism negative regulation of immune response regulation of innate immune response negative regulation of immune effector process negative regulation of humoral immune response response to external stimulus immune effector process regulation of response to stimulus defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response negative regulation of complement activation, alternative pathway regulation of complement activation activation of immune response regulation of defense response humoral immune response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus positive regulation of biological process negative regulation of complement activation positive regulation of response to stimulus response to stress regulation of response to stress innate immune response response to external biotic stimulus negative regulation of response to stimulus defense response biological regulation defense response to symbiont negative regulation of immune system process immune system process negative regulation of innate immune response multicellular organismal process regulation of cellular process negative regulation of interleukin-2 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of interleukin-2 production negative regulation of metabolic process interleukin-2 production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process negative regulation of lymphocyte proliferation regulation of leukocyte activation regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of macrophage activation myeloid leukocyte activation macrophage activation negative regulation of macrophage activation	cellular anatomical structure membrane protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth A]	IPR003598	Immunoglobulin subtype 2	Domain
B [auth A]	IPR039944	VSIG4, immunoglobulin variable (IgV)-like domain	Domain
B [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth A]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth A]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth A]	IPR039939	V-set and immunoglobulin domain-containing protein 4	Family
B [auth A]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A]	Pharos: Q9Y279	acute myeloid leukemia IgA glomerulonephritis non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma adrenal cortex carcinoma congestive heart failure head and neck cancer interstitial cystitis lung adenocarcinoma malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm Acute Myeloid Leukemia (AML-M2) astrocytic tumor acute myeloid leukemia IgA glomerulonephritis non-small cell lung carcinoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma adrenal cortex carcinoma congestive heart failure head and neck cancer interstitial cystitis lung adenocarcinoma malignant colon neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm Acute Myeloid Leukemia (AML-M2) astrocytic tumor Duchenne muscular dystrophy hepatocellular carcinoma invasive ductal breast carcinoma lung cancer medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia chronic obstructive pulmonary disease glioblastoma large cell medulloblastoma lung carcinoma

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.