5DMK | pdb_00005dmk

Crystal Structure of IAg7 in complex with RLGL-WE14

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5dmkc2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5dmkc1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5dmke2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5dmke1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d5dmkg2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d5dmkg1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5dmka2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5dmka1	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	MHC antigen-recognition domain	8055622	3000521	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054729	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054729	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	MHC antigen-recognition domain	8055622	3000521	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054729	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8055622	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8055622	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054729	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MHC antigen-recognition domain	8034745	3000521	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054689	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054689	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	MHC antigen-recognition domain	8034745	3000521	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	MHC antigen-recognition domain	8034745	3000521	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054689	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8034745	3000521	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054689	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)
H	C1-set_2	e5dmkH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
H	MHC_II_beta	e5dmkH2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_beta	ECOD (1.6)
F	C1-set_2	e5dmkF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
F	MHC_II_beta	e5dmkF2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_beta	ECOD (1.6)
D	C1-set_2	e5dmkD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
D	MHC_II_beta	e5dmkD2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_beta	ECOD (1.6)
B	C1-set_2	e5dmkB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
B	MHC_II_beta	e5dmkB2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_beta	ECOD (1.6)
C	C1-set_2	e5dmkC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
C	MHC_II_alpha	e5dmkC2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_alpha	ECOD (1.6)
E	C1-set_2	e5dmkE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
E	MHC_II_alpha	e5dmkE1	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_alpha	ECOD (1.6)
G	C1-set_2	e5dmkG1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
G	MHC_II_alpha	e5dmkG2	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_alpha	ECOD (1.6)
A	C1-set_2	e5dmkA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_2	ECOD (1.6)
A	MHC_II_alpha	e5dmkA1	A: a+b two layers	X: MHC antigen-recognition domain (From Topology)	H: MHC antigen-recognition domain (From Topology)	T: MHC antigen-recognition domain	F: MHC_II_alpha	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
G	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
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
B, D, F, H	IAg7 MH2, H2-Ab1 peptide	PEPTIDE-II-BETA	Mus musculus (house mouse)	H2-AB-NOD	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202605-0)
A, C, E, G	IAg7 MH2, H2-Ab1 peptide	II-ALPHA	Mus musculus (house mouse)	MH2-AAd	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202605-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, C, E, G	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein	-	positive regulation of dense core granule biogenesis regulation of biological process regulation of cellular process regulation of dense core granule biogenesis positive regulation of cellular component biogenesis biological regulation positive regulation of biological process regulation of cellular component biogenesis cellular component biogenesis cellular process cellular component organization or biogenesis dense core granule biogenesis positive regulation of cellular process heart process positive regulation of dense core granule biogenesis regulation of biological process regulation of cellular process regulation of dense core granule biogenesis positive regulation of cellular component biogenesis biological regulation positive regulation of biological process regulation of cellular component biogenesis cellular component biogenesis cellular process cellular component organization or biogenesis dense core granule biogenesis positive regulation of cellular process heart process multicellular organismal process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction regulation of the force of heart contraction blood circulation monoamine transport regulation of localization nitrogen compound transport negative regulation of amine transport regulation of catecholamine secretion transport negative regulation of biological process negative regulation of transport organic hydroxy compound transport localization secretion by cell regulation of secretion by cell negative regulation of secretion catecholamine transport negative regulation of cellular process negative regulation of secretion by cell secretion regulation of transport export from cell negative regulation of catecholamine secretion establishment of localization regulation of secretion catecholamine secretion amine transport regulation of amine transport regulation of tube diameter regulation of tube size positive regulation of vasoconstriction vascular process in circulatory system regulation of vasoconstriction positive regulation of multicellular organismal process blood vessel diameter maintenance vasoconstriction regulation of anatomical structure size inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis regulation of cytosolic calcium ion concentration cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cell chemotaxis cellular response to stimulus chemotaxis mast cell migration leukocyte migration cellular response to chemical stimulus taxis immune system process response to chemical mast cell chemotaxis myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion negative regulation of protein transport establishment of protein localization cell communication negative regulation of hormone secretion intracellular protein localization regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion negative regulation of protein secretion regulation of hormone secretion regulation of protein localization regulation of peptide secretion signaling negative regulation of signaling hormone secretion negative regulation of cell communication protein localization to extracellular region negative regulation of peptide secretion peptide secretion signal release negative regulation of protein localization regulation of signaling regulation of peptide transport regulation of establishment of protein localization cell-cell signaling regulation of protein transport peptide transport negative regulation of insulin secretion protein transport regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of response to stimulus signal transduction regulation of G protein-coupled receptor signaling pathway positive regulation of G protein-coupled receptor signaling pathway positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway regulation of response to stimulus G protein-coupled receptor signaling pathway regulation of phospholipase C-activating G protein-coupled receptor signaling pathway positive regulation of signaling establishment of organelle localization regulated exocytosis cellular localization cell activation involved in immune response leukocyte degranulation myeloid leukocyte activation myeloid leukocyte mediated immunity vesicle-mediated transport leukocyte activation organelle localization leukocyte activation involved in immune response establishment of localization in cell mast cell activation leukocyte mediated immunity mast cell mediated immunity immune response cell activation vacuolar localization mast cell degranulation myeloid cell activation involved in immune response immune effector process mast cell activation involved in immune response exocytosis lysosome localization relaxation of cardiac muscle regulation of relaxation of cardiac muscle regulation of muscle system process muscle system process relaxation of muscle positive regulation of relaxation of muscle positive regulation of relaxation of cardiac muscle regulation of relaxation of muscle defense response to Gram-negative bacterium intracellular signal transduction positive regulation of cAMP/PKA signal transduction cAMP/PKA signal transduction regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction regulation of cAMP/PKA signal transduction positive regulation of blood circulation positive regulation of cardiac muscle contraction cardiac muscle contraction striated muscle contraction positive regulation of striated muscle contraction regulation of cardiac muscle contraction muscle contraction positive regulation of heart contraction regulation of striated muscle contraction regulation of muscle contraction positive regulation of muscle contraction protein localization to organelle protein localization to secretory granule defense response to Gram-positive bacterium adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen	membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle neuronal dense core vesicle transport vesicle perinuclear region of cytoplasm extracellular region extracellular space chromaffin granule early endosome endosome Golgi apparatus cell surface MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex late endosome multivesicular body
A, C, E, G	H-2 class II histocompatibility antigen, A-D alpha chain	binding antigen binding peptide antigen binding peptide binding	response to stimulus immune response immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen multicellular organismal process regulation of leukocyte differentiation regulation of cellular process response to stimulus immune response immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of peptide antigen antigen processing and presentation of exogenous antigen multicellular organismal process regulation of leukocyte differentiation regulation of cellular process regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell activation T cell activation cell differentiation anatomical structure development positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process developmental process regulation of biological process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process regulation of developmental process positive regulation of biological process cell development positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis positive regulation of cell differentiation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation regulation of hemopoiesis cellular process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle intracellular organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane MHC protein complex MHC class II protein complex protein-containing complex plasma membrane protein complex membrane protein complex membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR001819	Chromogranin A/B	Family
B, D, F, H	IPR018054	Chromogranin, conserved site	Conserved Site
B, D, F, H	IPR001990	Chromogranin A/B/C	Family
B, D, F, H	IPR000353	MHC class II, beta chain, N-terminal	Domain
B, D, F, H	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B, D, F, H	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B, D, F, H	IPR003597	Immunoglobulin C1-set	Domain
B, D, F, H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B, D, F, H	IPR007110	Immunoglobulin-like domain	Domain
B, D, F, H	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, C, E, G	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A, C, E, G	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A, C, E, G	IPR003597	Immunoglobulin C1-set	Domain
A, C, E, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, C, E, G	IPR007110	Immunoglobulin-like domain	Domain
A, C, E, G	IPR001003	MHC class II, alpha chain, N-terminal	Domain
A, C, E, G	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site