5YXK

High resolution crystal structure of Human B7-2 IgV domain in P21 space group

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5yxka1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD86 (b7-2), N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5yxka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5yxkb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD86 (b7-2), N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5yxkb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5yxkc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD86 (b7-2), N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5yxkc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5yxkd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	CD86 (b7-2), N-terminal domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5yxkd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054505	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054505	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054505	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054505	3000071	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	V-set_9	e5yxkA1	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)
B	V-set_9	e5yxkB1	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)
C	V-set_9	e5yxkC1	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)
D	V-set_9	e5yxkD1	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	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	T-lymphocyte activation antigen CD86	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity signaling receptor activity coreceptor activity molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	response to stimulus immune response immune system process adaptive immune response multicellular organismal process B cell activation cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism response to stimulus immune response immune system process adaptive immune response multicellular organismal process B cell activation cell activation cellular process lymphocyte activation leukocyte activation cellular response to stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation positive regulation of T cell differentiation alpha-beta T cell differentiation involved in immune response regulation of cell development multicellular organism development type 2 immune response positive regulation of immune response T cell activation cell differentiation regulation of type 2 immune response regulation of T-helper cell differentiation alpha-beta T cell activation regulation of immune system process positive regulation of CD4-positive, alpha-beta T cell differentiation T-helper cell differentiation positive regulation of cell development immune effector process regulation of response to stimulus regulation of leukocyte cell-cell adhesion positive regulation of alpha-beta T cell differentiation regulation of developmental process cell development positive regulation of leukocyte cell-cell adhesion CD4-positive, alpha-beta T cell differentiation positive regulation of T-helper cell differentiation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation alpha-beta T cell differentiation T cell activation involved in immune response positive regulation of cell differentiation leukocyte activation involved in immune response regulation of T-helper 2 cell differentiation positive regulation of immune effector process regulation of cell-cell adhesion positive regulation of cellular process hemopoiesis regulation of cell adhesion positive regulation of T-helper 2 cell differentiation regulation of CD4-positive, alpha-beta T cell activation regulation of lymphocyte activation regulation of immune effector process regulation of leukocyte differentiation regulation of cellular process mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response positive regulation of developmental process positive regulation of cell activation anatomical structure development positive regulation of leukocyte activation T cell differentiation positive regulation of immune system process developmental process regulation of biological process positive regulation of T cell activation positive regulation of alpha-beta T cell activation regulation of immune response positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process positive regulation of biological process regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation leukocyte cell-cell adhesion positive regulation of response to stimulus positive regulation of CD4-positive, alpha-beta T cell activation cell adhesion cell-cell adhesion alpha-beta T cell activation involved in immune response positive regulation of hemopoiesis CD4-positive, alpha-beta T cell activation T-helper 2 cell differentiation regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion biological regulation regulation of T cell activation T cell differentiation involved in immune response positive regulation of type 2 immune response regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation cell surface receptor signaling pathway signaling cell communication CD40 signaling pathway signal transduction cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of molecular function positive regulation of kinase activity activation of protein kinase C activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of molecular function positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity organonitrogen compound metabolic process positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation immunoglobulin production cellular biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of immunoglobulin production positive regulation of gene expression positive regulation of production of molecular mediator of immune response regulation of macromolecule biosynthetic process regulation of production of molecular mediator of immune response positive regulation of cellular biosynthetic process regulation of cytokine production cytokine production regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production positive regulation of cytokine production organonitrogen compound biosynthetic process positive regulation of tumor necrosis factor superfamily cytokine production regulation of lymphotoxin A production lymphotoxin A production tumor necrosis factor superfamily cytokine production positive regulation of lymphotoxin A production regulation of tumor necrosis factor superfamily cytokine production positive regulation of DNA-templated transcription RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process positive regulation of nucleobase-containing compound metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction regulation of cell communication positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling lymphocyte costimulation T cell costimulation regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production lymphocyte proliferation regulation of leukocyte proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation mononuclear cell proliferation positive regulation of leukocyte proliferation 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 extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite intracellular non-membrane-bounded organelle microtubule cytoskeleton non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR013106	Immunoglobulin V-set domain	Domain
A, B, C, D	IPR003599	Immunoglobulin domain subtype	Domain
A, B, C, D	IPR051713	T-cell Activation and Immune Regulation Protein	Family
A, B, C, D	IPR037677	CD86, IgV domain	Domain
A, B, C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P42081	plasma cell myeloma liver disease Liver Cirrhosis, Experimental contact dermatitis invasive ductal breast carcinoma lung carcinoma malignant glioma myeloid neoplasm arthritic joint disease pilocytic astrocytoma cancer psoriasis diffuse large B-cell lymphoma Sjogren syndrome follicular lymphoma plasma cell myeloma liver disease Liver Cirrhosis, Experimental contact dermatitis invasive ductal breast carcinoma lung carcinoma malignant glioma myeloid neoplasm arthritic joint disease pilocytic astrocytoma cancer psoriasis diffuse large B-cell lymphoma Sjogren syndrome follicular lymphoma ulcerative colitis glioblastoma hematologic disease juvenile idiopathic arthritis lung disease malignant mesothelioma non-small cell lung carcinoma autoimmune disease chronic obstructive pulmonary disease cutaneous lupus erythematosus digestive system neuroendocrine neoplasm skin disease gastric cancer X-linked mixed deafness with perilymphatic gusher Hashimoto thyroiditis interstitial cystitis lung cancer lymphatic system disease medulloblastoma pancreatic intraductal papillary-mucinous carcinoma breast cancer plasma cell neoplasm cystic fibrosis rheumatoid arthritis subependymal giant cell astrocytoma gastric carcinoma head and neck cancer

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Channels: Other Ion Channels	GluN1a/GluN2B NMDA receptor, apo-form crystal structure

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.