2NNA | pdb_00002nna

Structure of the MHC class II molecule HLA-DQ8 bound with a deamidated gluten 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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2nnab1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nnab2	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	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2nnab3	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	8054679	3000071	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8041502	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8034484	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055664	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	TetR_N	e2nnaA1	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: TetR_N	ECOD (v294.1)
B	CBS	e2nnaB3	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: CBS	ECOD (v294.1)
B	Rieske	e2nnaB2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Rieske	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

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	pMHC-II, HLA-DQA10301_HLA-DQB10302	II-ALPHA	Homo sapiens (human)	HLA-DQA10301, HLA-DQA10302, HLA-DQA1*0303	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202611-0)
B	pMHC-II, HLA-DQA10301_HLA-DQB10302	PEPTIDE-II-BETA	Homo sapiens (human)	HLA-DQB1*0302	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_PEPTIDE-BETA	IMGT (202611-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Source
A	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	Domain
A	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain	Domain
B	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain	Domain
B	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	MHC class II antigen	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	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	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment lumenal side of endoplasmic reticulum membrane side of membrane lumenal side of membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane Golgi apparatus Golgi apparatus subcompartment trans-Golgi network membrane trans-Golgi network transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane
B	MHC class II antigen	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	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 cellular response to stimulus immune response-regulating cell surface receptor signaling pathway 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 cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling cell communication immune response-activating signaling pathway immune response-regulating signaling pathway signal transduction cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response humoral 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 MHC protein complex assembly cellular component organization or biogenesis multicellular organismal 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	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane MHC protein complex cell periphery MHC class II protein complex protein-containing complex plasma membrane protein complex plasma membrane membrane protein complex endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment lumenal side of endoplasmic reticulum membrane side of membrane lumenal side of membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane Golgi apparatus Golgi apparatus subcompartment trans-Golgi network membrane trans-Golgi network transport vesicle transport vesicle membrane COPII-coated ER to Golgi transport vesicle ER to Golgi transport vesicle membrane
C	gluten peptide	nutrient reservoir activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
A	IPR003597	Immunoglobulin C1-set	Domain
A	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR007110	Immunoglobulin-like domain	Domain
A	IPR001003	MHC class II, alpha chain, N-terminal	Domain
B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
B	IPR003597	Immunoglobulin C1-set	Domain
B	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B	IPR000353	MHC class II, beta chain, N-terminal	Domain
B	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR007110	Immunoglobulin-like domain	Domain
C	IPR001954	Gliadin/LMW glutenin	Family
C	IPR036312	Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily	Homologous Superfamily
C	IPR016140	Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P01909	membranous glomerulonephritis achalasia type 1 diabetes mellitus oropharynx cancer systemic lupus erythematosus celiac disease eosinophilia-myalgia syndrome visceral leishmaniasis pancreatitis ulcerative colitis asthma juvenile idiopathic arthritis narcolepsy B-cell chronic lymphocytic leukemia Sjogren syndrome membranous glomerulonephritis achalasia type 1 diabetes mellitus oropharynx cancer systemic lupus erythematosus celiac disease eosinophilia-myalgia syndrome visceral leishmaniasis pancreatitis ulcerative colitis asthma juvenile idiopathic arthritis narcolepsy B-cell chronic lymphocytic leukemia Sjogren syndrome lung carcinoma alopecia areata proteinuria dermatitis megaesophagus allergic disease chronic obstructive pulmonary disease Crohn disease squamous cell carcinoma Diabetes Mellitus, Insulin-Dependent lymphoma systemic sclerosis tuberculosis mycobacterium tuberculosis, susceptibility to Hashimoto thyroiditis neoplasm of mature B-cells allergic rhinitis hepatitis B virus infection neuromyelitis optica atopic eczema oral cavity cancer idiopathic achalasia celiac disease, susceptibility to, 1 inflammatory bowel disease primary biliary cholangitis rheumatoid arthritis colorectal adenoma leprosy cutaneous lupus erythematosus squamous cell lung carcinoma malignant glioma Takayasu arteritis Duchenne muscular dystrophy metabolic syndrome X vitiligo glioblastoma nasal cavity disease acquired metabolic disease head and neck cancer neoplasm of oropharynx hepatitis C virus infection non-alcoholic fatty liver disease autism spectrum disorder idiopathic membranous glomerulonephritis pemphigus vulgaris cervical cancer invasive ductal breast carcinoma rosacea colorectal cancer skin basal cell carcinoma temporal arteritis endogenous depression myasthenia gravis eosinophilic granulomatosis with polyangiitis myositis Graves disease nasopharyngeal disease head and neck squamous cell carcinoma nephrotic syndrome hepatocellular carcinoma non-small cell lung carcinoma autoimmune disease hypothyroidism ovarian cancer IgA glomerulonephritis peripheral arterial disease psoriatic arthritis sinusitis lung cancer
B	Pharos: P01920	narcolepsy achalasia oropharynx cancer urticaria angioedema celiac disease type 1 diabetes mellitus IgA glomerulonephritis bullous pemphigoid systemic sclerosis megaesophagus Creutzfeldt Jacob disease Drug Eruptions narcolepsy-cataplexy syndrome juvenile idiopathic arthritis narcolepsy achalasia oropharynx cancer urticaria angioedema celiac disease type 1 diabetes mellitus IgA glomerulonephritis bullous pemphigoid systemic sclerosis megaesophagus Creutzfeldt Jacob disease Drug Eruptions narcolepsy-cataplexy syndrome juvenile idiopathic arthritis multiple sclerosis allergic disease asthma ulcerative colitis malignant colon neoplasm diffuse scleroderma narcolepsy without cataplexy nephrosclerosis ductal breast carcinoma in situ alopecia areata glioblastoma pancreatic intraductal papillary-mucinous carcinoma astrocytic tumor pilocytic astrocytoma breast carcinoma inherited Creutzfeldt-Jakob disease rosacea C1 inhibitor deficiency juvenile dermatomyositis subependymal giant cell astrocytoma cerebrovascular disorder large cell medulloblastoma tuberculosis lung carcinoma Crohn disease malignant pancreatic neoplasm multiple sclerosis, susceptibility to 1 drug-induced liver injury acquired metabolic disease esophageal adenocarcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor idiopathic achalasia pituitary cancer interstitial cystitis schizophrenia limb-girdle muscular dystrophy lymphoplasmacytic lymphoma cystic fibrosis medulloblastoma neoplasm of oropharynx Duchenne muscular dystrophy non-small cell lung carcinoma exocrine pancreatic carcinoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia autoimmune disease rheumatoid arthritis invasive ductal breast carcinoma Sjogren syndrome celiac disease, susceptibility to, 1 Kleine-Levin syndrome lung cancer