5YXK | pdb_00005yxk

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		e5yxkA1	A: alpha bundles	X: PriB N-terminal domain-like	H: HTH	T: SH3	F:	ECOD (develop294)
B	PLAT	e5yxkB1	A: alpha bundles	X: PriB N-terminal domain-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: PLAT	ECOD (develop294)
C	PLAT	e5yxkC1	A: alpha bundles	X: PriB N-terminal domain-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: PLAT	ECOD (develop294)
D	PLAT	e5yxkD1	A: alpha bundles	X: PriB N-terminal domain-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: PLAT	ECOD (develop294)

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 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 negative regulation of lymphocyte proliferation regulation of cellular process regulation of leukocyte activation negative regulation of biological process 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 immune system process regulation of leukocyte proliferation regulation of biological process 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 multicellular organismal process negative regulation of leukocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion biological regulation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of alpha-beta T cell activation positive regulation of T cell differentiation regulation of cell development multicellular organism development type 2 immune response positive regulation of immune response cell differentiation regulation of type 2 immune response regulation of T-helper cell differentiation alpha-beta T cell activation 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 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 positive regulation of immune effector process regulation of T-helper 2 cell differentiation positive regulation of cellular process hemopoiesis positive regulation of T-helper 2 cell differentiation regulation of CD4-positive, alpha-beta T cell activation regulation of immune effector process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation 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 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 positive regulation of response to stimulus positive regulation of CD4-positive, alpha-beta T cell activation 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 lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion 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 positive regulation of cell population proliferation positive regulation of cell communication immune response-regulating cell surface receptor signaling pathway positive regulation of signal transduction positive regulation of T cell receptor signaling pathway signaling regulation of antigen receptor-mediated signaling pathway regulation of signal transduction cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of T cell receptor signaling pathway T cell receptor signaling pathway regulation of cell communication antigen receptor-mediated signaling pathway activation of immune response positive regulation of antigen receptor-mediated signaling pathway positive regulation of signaling negative regulation of signaling negative regulation of antigen receptor-mediated signaling pathway negative regulation of cell communication negative regulation of response to stimulus negative regulation of signal transduction negative regulation of T cell receptor signaling pathway immunoglobulin production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of immunoglobulin production regulation of biosynthetic process production of molecular mediator of immune response regulation of macromolecule metabolic process gene expression macromolecule 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 metabolic process regulation of production of molecular mediator of immune response macromolecule metabolic process regulation of metabolic 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 positive regulation of protein metabolic process regulation of primary metabolic process positive regulation of tumor necrosis factor superfamily cytokine production protein metabolic process regulation of lymphotoxin A production lymphotoxin A production regulation of protein metabolic process tumor necrosis factor superfamily cytokine production primary metabolic process 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 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 regulation of non-canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction lymphocyte costimulation T cell costimulation regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of leukocyte proliferation positive regulation of mononuclear cell proliferation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane 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 membraneless organelle intracellular organelle centrosome microtubule organizing center cytoskeleton centriolar satellite membraneless organelle microtubule cytoskeleton

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 arthritic joint disease myeloid neoplasm cancer pilocytic astrocytoma 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 arthritic joint disease myeloid neoplasm cancer pilocytic astrocytoma psoriasis diffuse large B-cell lymphoma Sjogren syndrome follicular lymphoma ulcerative colitis glioblastoma hematologic disease juvenile idiopathic arthritis lung disease malignant mesothelioma autoimmune disease non-small cell lung carcinoma 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 breast cancer pancreatic intraductal papillary-mucinous carcinoma 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.