3ERY | pdb_00003ery

Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8034809	3000521	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8034809	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)
B	zf-CCCH_4	e3eryB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (v294.1)
A	zf-CCCH_4	e3eryA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: zf-CCCH_4	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
A	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	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, B	MH1 HLA-B*1557	G-ALPHA1-ALPHA2	Homo sapiens (human)	H2-Ld-2	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2	MH	(G-ALPHA1-ALPHA2)	IMGT (202611-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	H-2 class I histocompatibility antigen	binding antigen binding peptide antigen binding peptide binding protein binding protein-folding chaperone binding TAP1 binding TAP binding 14-3-3 protein binding natural killer cell lectin-like receptor binding signaling receptor binding TAP complex binding protein-containing complex binding beta-2-microglobulin binding binding antigen binding peptide antigen binding peptide binding protein binding protein-folding chaperone binding TAP1 binding TAP binding 14-3-3 protein binding natural killer cell lectin-like receptor binding signaling receptor binding TAP complex binding protein-containing complex binding beta-2-microglobulin binding T cell receptor binding identical protein binding CD8 receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein homodimerization activity protein dimerization activity MHC class I protein binding MHC protein binding TAP2 binding	antigen processing and presentation immune system process antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I response to stimulus defense response response to stress adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity antigen processing and presentation immune system process antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway antigen processing and presentation of endogenous peptide antigen antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent antigen processing and presentation of peptide antigen antigen processing and presentation of endogenous antigen antigen processing and presentation of endogenous peptide antigen via MHC class I response to stimulus defense response response to stress adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity regulation of immune effector process T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response positive regulation of leukocyte mediated cytotoxicity leukocyte mediated immunity regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process positive regulation of cellular process regulation of T cell mediated immunity T cell mediated cytotoxicity regulation of biological process positive regulation of T cell mediated cytotoxicity immune response regulation of adaptive immune response biological regulation regulation of leukocyte mediated cytotoxicity leukocyte mediated cytotoxicity adaptive immune response immune effector process regulation of leukocyte mediated immunity regulation of T cell mediated cytotoxicity regulation of lymphocyte mediated immunity regulation of response to stimulus positive regulation of T cell mediated immunity regulation of immune response regulation of cell killing cellular process positive regulation of cell killing cell killing antigen processing and presentation of endogenous peptide antigen via MHC class Ib antigen processing and presentation of peptide antigen via MHC class Ib antigen processing and presentation via MHC class Ib	membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane membrane-bounded organelle intracellular anatomical structure cis-Golgi network membrane Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure bounding membrane of organelle cis-Golgi network organelle cytoplasm organelle membrane cell periphery cell surface plasma membrane external side of plasma membrane side of membrane MHC class I protein complex MHC protein complex protein-containing complex plasma membrane protein complex membrane protein complex endoplasmic reticulum exit site endoplasmic reticulum MHC class Ib protein complex intracellular vesicle phagocytic vesicle phagocytic vesicle membrane cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane endocytic vesicle membrane vesicle endocytic vesicle vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi membrane MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane extracellular region extracellular space Golgi apparatus subcompartment Golgi cisterna Golgi stack Golgi medial cisterna early endosome endosome lumenal side of endoplasmic reticulum membrane lumenal side of membrane endosome membrane early endosome membrane
C [auth P], D [auth Q]	2-oxoglutarate dehydrogenase E1 peptide	protein binding binding heat shock protein binding protein-folding chaperone binding cation binding vitamin binding thiamine pyrophosphate binding ion binding anion binding quaternary ammonium group binding heterocyclic compound binding small molecule binding sulfur compound binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor protein binding binding heat shock protein binding protein-folding chaperone binding cation binding vitamin binding thiamine pyrophosphate binding ion binding anion binding quaternary ammonium group binding heterocyclic compound binding small molecule binding sulfur compound binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxoglutarate dehydrogenase (succinyl-transferring) activity catalytic activity metal ion binding	developmental process multicellular organismal process head development animal organ development brain development nervous system development cerebellar cortex development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development developmental process multicellular organismal process head development animal organ development brain development nervous system development cerebellar cortex development multicellular organism development cerebellum development central nervous system development metencephalon development anatomical structure development hindbrain development system development forebrain development olfactory lobe development tangential migration from the subventricular zone to the olfactory bulb telencephalon cell migration forebrain cell migration cell migration cellular process telencephalon development cell motility olfactory bulb development pallium development hippocampus development limbic system development pyramidal neuron development cellular developmental process central nervous system neuron development cell development central nervous system neuron differentiation neurogenesis neuron differentiation cell differentiation forebrain generation of neurons generation of neurons forebrain neuron development neuron development forebrain neuron differentiation pyramidal neuron differentiation nucleoside phosphate metabolic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process metabolic process small molecule metabolic process succinyl-CoA metabolic process phosphorus metabolic process generation of precursor metabolites and energy diencephalon development thalamus development aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds ribonucleotide catabolic process pyridine nucleotide catabolic process oxoacid metabolic process carbohydrate catabolic process carbohydrate derivative metabolic process organophosphate catabolic process nucleoside phosphate catabolic process organic acid metabolic process glycolytic process pyridine-containing compound metabolic process purine ribonucleotide catabolic process nicotinamide nucleotide metabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process catabolic process ATP metabolic process purine nucleotide metabolic process ribonucleotide metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process ADP metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process olfactory bulb mitral cell layer development 2-oxoglutarate metabolic process succinyl-CoA biosynthetic process 2-oxoglutarate decarboxylation to succinyl-CoA purine-containing compound biosynthetic process acyl-CoA biosynthetic process dicarboxylic acid metabolic process nucleobase-containing compound biosynthetic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process striatum development subpallium development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane membrane organelle envelope mitochondrial envelope organelle membrane protein-containing complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial membrane membrane organelle envelope mitochondrial envelope organelle membrane protein-containing complex oxoglutarate dehydrogenase complex catalytic complex oxidoreductase complex transferase complex tricarboxylic acid cycle heteromeric enzyme complex alpha-ketoacid dehydrogenase complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR010579	MHC class I, alpha chain, C-terminal	Domain
A, B	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, B	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
A, B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR050208	Antigen-presenting and immune regulatory MHC class I-related	Family
A, B	IPR003597	Immunoglobulin C1-set	Domain
A, B	IPR011161	MHC class I-like antigen recognition-like	Domain
A, B	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
C [auth P], D [auth Q]	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily	Homologous Superfamily
C [auth P], D [auth Q]	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
C [auth P], D [auth Q]	IPR001017	Dehydrogenase, E1 component	Domain
C [auth P], D [auth Q]	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
C [auth P], D [auth Q]	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain	Domain
C [auth P], D [auth Q]	IPR011603	2-oxoglutarate dehydrogenase E1 component	Family
C [auth P], D [auth Q]	IPR031717	2-oxoglutarate dehydrogenase E1 component/KDG, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth P], D [auth Q]	Pharos: Q02218	oxoglutaricaciduria astrocytic tumor glioblastoma malignant mesothelioma oligodendroglioma psoriasis dermatomyositis large cell medulloblastoma medulloblastoma ovarian cancer drug-induced liver injury malignant ependymoma Mitochondrial Diseases

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.