5YMV

Crystal structure of 9-mer peptide from influenza virus in complex with BF2*1201

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8070475	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8070475	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	PF07654	e5ymvA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
A	PF00129	e5ymvA2	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: PF00129	ECOD (1.6)
D	PF07654	e5ymvD2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D	PF00129	e5ymvD1	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: PF00129	ECOD (1.6)
B	PF07654	e5ymvB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E	PF07654	e5ymvE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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)
D	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)
E	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, D	MH1 MH1-B*2401	I-ALPHA	Gallus gallus (chicken)	MH1-B*2401	G-DOMAIN G-ALPHA1, G-DOMAIN G-ALPHA2, C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202416-0)
B, E	MH1 MH1-B*2401	B2M	Gallus gallus (chicken)	B2M*01	C-LIKE-DOMAIN C-LIKE	MH	MH1-ALPHA_B2M	IMGT (202416-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF00129	Class I Histocompatibility antigen, domains alpha 1 and 2 (MHC_I)	Class I Histocompatibility antigen, domains alpha 1 and 2	-	Domain
A, D	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B, E	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, D	Class I histocompatibility antigen, F10 alpha chain	-	response to stimulus immune response immune system process antigen processing and presentation antigen processing and presentation of peptide antigen via MHC class I antigen processing and presentation of peptide antigen	cell periphery cell surface membrane plasma membrane cellular anatomical entity 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 extracellular region extracellular space
B, E	Beta-2-microglobulin	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex binding identical protein binding protein binding protein homodimerization activity protein dimerization activity structural molecule activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis regulation of biological process response to stimulus immune response biological regulation intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis 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 based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity regulation of cellular process T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process cytokine production organic substance biosynthetic process leukocyte mediated immunity positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production regulation of T cell mediated immunity regulation of cytokine production involved in immune response regulation of adaptive immune response cellular metabolic process regulation of cellular metabolic process immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic 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 cellular biosynthetic process positive regulation of cellular metabolic process regulation of T cell cytokine production organic substance metabolic process regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response positive regulation of cellular process production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of cellular biosynthetic process regulation of lymphocyte mediated immunity positive regulation of gene expression positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response cellular process positive regulation of cellular biosynthetic process organonitrogen compound metabolic process primary metabolic process amyloid fibril formation cellular component organization protein metabolic process cellular component organization or biogenesis supramolecular fiber organization cellular response to stimulus cellular response to inorganic substance cellular response to metal ion response to inorganic substance cellular response to iron ion cellular response to chemical stimulus response to metal ion response to chemical response to iron ion protein-containing complex organization protein homotetramerization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly protein homooligomerization 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 peptide antigen assembly with MHC protein complex MHC class II protein complex assembly MHC protein complex assembly cellular response to nicotine response to nicotine regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport localization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis regulation of cellular senescence cellular senescence positive regulation of cellular senescence cellular response to stress response to stress 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 antigen antigen processing and presentation of endogenous peptide antigen via MHC class I behavior system process learning or memory nervous system process cognition peptide antigen assembly with MHC class I protein complex MHC class I protein complex assembly regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis multicellular organism development neurogenesis cell differentiation anatomical structure development negative regulation of cellular process negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process nervous system development negative regulation of cell development negative regulation of multicellular organismal process negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation 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 cell-cell adhesion 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 regulation of lymphocyte activation negative regulation of forebrain neuron differentiation forebrain development regulation of forebrain neuron differentiation central nervous system neuron differentiation neuron differentiation head development forebrain generation of neurons animal organ development brain development generation of neurons central nervous system development forebrain neuron differentiation negative regulation of neuron differentiation regulation of neuron differentiation regulation of monoatomic ion transport regulation of iron ion transport iron ion transport metal ion transport monoatomic ion transport transition metal ion transport regulation of metal ion transport monoatomic cation transport	cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex cellular anatomical entity receptor complex intracellular anatomical structure cytoplasm cytosol MHC protein complex cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex HFE-transferrin receptor complex cellular anatomical entity receptor complex intracellular anatomical structure cytoplasm cytosol MHC protein complex MHC class II protein complex MHC class I protein complex membrane-bounded organelle endosome membrane 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 vesicle organelle membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus extracellular region MHC class I peptide loading complex organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane
C, F	ALA-VAL-LYS-GLY-VAL-GLY-THR-MET-VAL	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, D	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A, D	IPR003597	Immunoglobulin C1-set	Domain
A, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, D	IPR011161	MHC class I-like antigen recognition-like	Domain
A, D	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
A, D	IPR007110	Immunoglobulin-like domain	Domain
A, D	IPR001039	MHC class I alpha chain, alpha1 alpha2 domains	Domain
A, D	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, E	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, E	IPR003597	Immunoglobulin C1-set	Domain
B, E	IPR015707	Beta-2-Microglobulin	Family
B, E	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B, E	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, E	IPR007110	Immunoglobulin-like domain	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 R01GM133198.