1KT2 | pdb_00001kt2

CRYSTAL STRUCTURE OF CLASS II MHC MOLECULE IEK BOUND TO MOTH CYTOCHROME C PEPTIDE

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)
D	d1kt2d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	(Lonomia obliqua ) [TaxId: 304329 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d1kt2d2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC beta chain, N-terminal domain	(Lonomia obliqua ) [TaxId: 304329 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1kt2b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	(Lonomia obliqua ) [TaxId: 304329 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1kt2b2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC beta chain, N-terminal domain	(Lonomia obliqua ) [TaxId: 304329 ], house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1kt2a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1kt2a2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC alpha chain, N-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1kt2c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC alpha chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1kt2c2	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	Class II MHC alpha chain, N-terminal domain	house mouse (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)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8055626	3000521	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054713	3000071	SCOP2B (2022-06-29)
B	SCOP2 Family	C1 set domains-like	8054712	4000202	SCOP2 (2022-06-29)
B	SCOP2 Family	MHC antigen-recognition domain	8055625	4001031	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054713	3000071	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	MHC antigen-recognition domain	8055626	3000521	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8055642	3000521	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054675	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054675	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MHC antigen-recognition domain	8055642	3000521	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)
D	Copper-bind	e1kt2D1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D	MHC_II_beta	e1kt2D2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MHC_II_beta	ECOD (v294.1)
B	Copper-bind	e1kt2B1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
B	MHC_II_beta	e1kt2B2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MHC_II_beta	ECOD (v294.1)
A	Copper-bind	e1kt2A1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
A	MHC_I_3	e1kt2A2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: MHC_I_3	ECOD (v294.1)
C	Copper-bind	e1kt2C1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
C	MHC_I_3	e1kt2C2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: MHC_I_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

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	pMHC100	PEPTIDE-II-BETA	Mus musculus (house mouse)	H2-EB1k	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202612-0)
A, C	pMHC100	II-ALPHA	Mus musculus (house mouse)	MH2-AAe, H2-EAck, H2-EAk	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202612-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain		Domain
B, D	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, C	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A, C	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	Fusion protein consisting of cytochrome C peptide, glycine rich linker, and MHC E-beta-k	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity MHC class II receptor activity immune receptor activity protein binding signaling receptor binding binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity MHC class II receptor activity immune receptor activity protein binding signaling receptor binding CD4 receptor binding polysaccharide binding carbohydrate binding T cell receptor binding	regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of immune system process adaptive immune response antigen processing and presentation of exogenous peptide antigen via MHC class II regulation of biological process response to stimulus immune response biological regulation positive regulation of biological process positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus immune system process regulation of immune response regulation of immune system process positive regulation of 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 peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular process MHC protein complex assembly cellular component organization or biogenesis multicellular organismal process regulation of cellular process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process 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 endosome membrane 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 endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane immunological synapse vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome
A, C	H-2 class II histocompatibility antigen, E-D alpha chain	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding polysaccharide binding carbohydrate binding protein binding signaling receptor binding T cell receptor binding	multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion multicellular organismal process regulation of cellular process regulation of alpha-beta T cell activation regulation of leukocyte activation positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of CD4-positive, alpha-beta T cell activation positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation CD4-positive, alpha-beta T cell activation positive regulation of leukocyte activation alpha-beta T cell activation regulation of immune system process regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation positive regulation of alpha-beta T cell activation regulation of CD4-positive, alpha-beta T cell activation immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process cellular process regulation of lymphocyte activation response to stimulus immune response positive regulation of response to stimulus positive regulation of immune response regulation of response to stimulus regulation of immune response antigen processing and presentation antigen processing and presentation of peptide or polysaccharide antigen via MHC class II 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 adaptive immune response immune effector process antigen processing and presentation of endogenous peptide antigen via MHC class II antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class II antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of exogenous peptide antigen via MHC class II antigen processing and presentation of exogenous peptide antigen antigen processing and presentation of exogenous antigen system process nervous system process cognition peptide antigen assembly with MHC class II protein complex protein-containing complex organization peptide antigen assembly with MHC protein complex MHC class II protein complex assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly MHC protein complex assembly cellular component organization or biogenesis dendritic cell antigen processing and presentation myeloid dendritic cell antigen processing and presentation regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of leukocyte mediated cytotoxicity positive regulation of immune effector process positive regulation of adaptive immune response regulation of T cell mediated immunity T cell mediated cytotoxicity positive regulation of T cell mediated cytotoxicity regulation of adaptive immune response regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity positive regulation of T cell mediated immunity regulation of cell killing positive regulation of cell killing cell killing regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation regulation of cell development multicellular organism development cell differentiation regulation of T-helper cell differentiation anatomical structure development T cell differentiation developmental process T-helper cell differentiation leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of hemopoiesis immunological memory formation process cell activation involved in immune response positive regulation of T cell differentiation positive regulation of developmental process positive regulation of memory T cell differentiation positive regulation of cell development memory T cell differentiation T cell activation involved in immune response positive regulation of hemopoiesis positive regulation of cell differentiation leukocyte activation involved in immune response lymphocyte activation involved in immune response T cell differentiation involved in immune response regulation of memory T cell differentiation immunological memory process positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation positive regulation of CD4-positive, alpha-beta T cell differentiation positive regulation of regulatory T cell differentiation regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation positive regulation of alpha-beta T cell differentiation positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation regulation of regulatory T cell differentiation CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation regulatory T cell differentiation	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 endosome membrane 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 endosome membrane intracellular anatomical structure endosome intracellular vesicle late endosome membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle late endosome cytoplasm vesicle organelle membrane lytic vacuole vacuole lysosome immunological synapse vacuolar membrane lytic vacuole membrane lysosomal membrane

InterPro: Protein Family Classification InterPro Database Homepage

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

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.