1D9K | pdb_00001d9k

CRYSTAL STRUCTURE OF COMPLEX BETWEEN D10 TCR AND PMHC I-AK/CA

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)
F [auth E]	d1d9ke_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d1d9ka_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1d9kb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth F]	d1d9kf_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	T-cell antigen receptor	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d1d9kc1	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	d1d9kc2	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)
H [auth G]	d1d9kg1	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)
H [auth G]	d1d9kg2	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)
D	d1d9kd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d1d9kd2	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	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
I [auth H]	d1d9kh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Class II MHC beta chain, C-terminal domain	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
I [auth H]	d1d9kh2	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	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)
F [auth E]	SCOP2 Family	V set domains-like	8103347	4007530	SCOP2 (2022-06-29)
F [auth E]	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8103348	3000071	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8103348	3000071	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	3000071	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055394	3000071	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	MHC antigen-recognition domain	8034741	3000521	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054681	3000071	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	MHC antigen-recognition domain	8034741	3000521	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054681	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054719	3000071	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	MHC antigen-recognition domain	8034738	3000521	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	MHC antigen-recognition domain	8034738	3000521	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054719	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)
F [auth E]	Copper-bind	e1d9kE1	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	Copper-bind	e1d9kA1	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	Copper-bind	e1d9kC1	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	e1d9kC2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: MHC_I_3	ECOD (v294.1)
H [auth G]	Copper-bind	e1d9kG1	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)
H [auth G]	MHC_I_3	e1d9kG2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: MHC_I_3	ECOD (v294.1)
D	Copper-bind	e1d9kD1	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	Glyco_hydro_32C	e1d9kD2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Glyco_hydro_32C	ECOD (v294.1)
I [auth H]	Copper-bind	e1d9kH1	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)
I [auth H]	Glyco_hydro_32C	e1d9kH2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: Glyco_hydro_32C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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)
G [auth F]	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)
H [auth G]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
H [auth G]	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)
I [auth H]	3.10.320.10	Alpha Beta	Roll	Class II Histocompatibility Antigen, M Beta Chain	Chain B, domain 1	CATH (4.3.0)
I [auth H]	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, F [auth E]	TR D10	V-ALPHA	Mus musculus (house mouse)	TRAV14D-201, TRAJ3901	V-DOMAIN V-ALPHA	TR	FV-ALPHA_BETA	IMGT (202613-0)
B, G [auth F]	TR D10	V-BETA	Mus musculus (house mouse)	TRBV13-201, TRBV13-203, TRBJ2-1*01	V-DOMAIN V-BETA	TR	FV-ALPHA_BETA	IMGT (202613-0)
C, H [auth G]	MH2-AA_MH2-ABk	II-ALPHA	Mus musculus (house mouse)	MH2-AA*02	G-DOMAIN G-ALPHA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_BETA	IMGT (202613-0)
D, I [auth H]	MH2-AA_MH2-ABk	II-BETA	Mus musculus (house mouse)	H2-ABk	G-DOMAIN G-BETA, C-LIKE-DOMAIN C-LIKE	MH	MH2-ALPHA_BETA	IMGT (202613-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, F [auth E]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B, G [auth F]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C, H [auth G]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C, H [auth G]	PF00993	Class II histocompatibility antigen, alpha domain (MHC_II_alpha)	Class II histocompatibility antigen, alpha domain		Domain
D, I [auth H]	PF00969	Class II histocompatibility antigen, beta domain (MHC_II_beta)	Class II histocompatibility antigen, beta domain		Domain
D, I [auth H]	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, F [auth E]	T-CELL RECEPTOR D10 (ALPHA CHAIN)	binding antigen binding peptide antigen binding peptide binding	response to stimulus immune response immune system process adaptive immune response	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex T cell receptor complex
B, G [auth F]	T-CELL RECEPTOR D10 (BETA CHAIN)	-	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex plasma membrane protein complex plasma membrane signaling receptor complex membrane protein complex signaling receptor complex T cell receptor complex
C, H [auth G]	MHC I-AK A CHAIN (ALPHA CHAIN)	binding antigen binding peptide antigen binding peptide binding protein-containing complex binding MHC protein complex binding MHC class II protein complex 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 negative regulation of lymphocyte proliferation multicellular organismal process regulation of cellular process regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion cell activation regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation cellular process regulation of lymphocyte activation 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 positive regulation of leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation positive regulation of cellular process positive regulation of T cell activation positive regulation of cell adhesion positive regulation of multicellular organismal process regulation of leukocyte differentiation 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 cell differentiation anatomical structure development T cell differentiation developmental process positive regulation of cell development leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte 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 vacuolar membrane lytic vacuole membrane lysosomal membrane
D, I [auth H]	MHC I-AK B CHAIN (BETA CHAIN)	-	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	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle Golgi apparatus membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle 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
E [auth P], J [auth Q]	CONALBUMIN PEPTIDE	cation binding ferric iron binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding	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 response to stimulus response to chemical response to xenobiotic stimulus localization 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 response to stimulus response to chemical response to xenobiotic stimulus localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport acute-phase response defense response response to stress inflammatory response acute inflammatory response humoral immune response biological process involved in interspecies interaction between organisms response to other organism immune response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to other organism immune system process response to external biotic stimulus monoatomic ion transmembrane transport iron ion transmembrane transport monoatomic cation transmembrane transport transmembrane transport cellular process antibacterial humoral response defense response to bacterium response to bacterium response to lipid response to oxygen-containing compound response to lipopolysaccharide response to molecule of bacterial origin	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle recycling endosome organomineral extracellular matrix extracellular matrix external encapsulating structure extracellular region specialized extracellular matrix cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, F [auth E]	IPR051006	T cell receptor variable domain	Family
A, F [auth E]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, F [auth E]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, F [auth E]	IPR013106	Immunoglobulin V-set domain	Domain
A, F [auth E]	IPR003599	Immunoglobulin domain subtype	Domain
A, F [auth E]	IPR007110	Immunoglobulin-like domain	Domain
B, G [auth F]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, G [auth F]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B, G [auth F]	IPR013106	Immunoglobulin V-set domain	Domain
B, G [auth F]	IPR003599	Immunoglobulin domain subtype	Domain
B, G [auth F]	IPR007110	Immunoglobulin-like domain	Domain
B, G [auth F]	IPR050413	T cell receptor beta variable	Family
C, H [auth G]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, H [auth G]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
C, H [auth G]	IPR003597	Immunoglobulin C1-set	Domain
C, H [auth G]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
C, H [auth G]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C, H [auth G]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
C, H [auth G]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, H [auth G]	IPR007110	Immunoglobulin-like domain	Domain
C, H [auth G]	IPR001003	MHC class II, alpha chain, N-terminal	Domain
D, I [auth H]	IPR000353	MHC class II, beta chain, N-terminal	Domain
D, I [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D, I [auth H]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
D, I [auth H]	IPR014745	MHC class II, alpha/beta chain, N-terminal	Homologous Superfamily
D, I [auth H]	IPR003597	Immunoglobulin C1-set	Domain
D, I [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D, I [auth H]	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily
D, I [auth H]	IPR007110	Immunoglobulin-like domain	Domain
D, I [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
E [auth P], J [auth Q]	IPR016357	Transferrin	Family
E [auth P], J [auth Q]	IPR001156	Transferrin-like domain	Domain
E [auth P], J [auth Q]	IPR018195	Transferrin family, iron binding site	Binding Site