1SY6 | pdb_00001sy6

Crystal Structure of CD3gammaepsilon Heterodimer in Complex with OKT3 Fab Fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab 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)
A [auth L]	d1sy6l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d1sy6l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1sy6h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1sy6h2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d1sy6h3	Artifacts	Tags	Tags	Tags	N-terminal Tags	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth A]	d1sy6a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	CD3 epsilon chain ectodomain fragment	human (Homo sapiens ) [TaxId: 9606 ], human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth A]	d1sy6a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	CD3 gamma chain ectodomain fragment	human (Homo sapiens ) [TaxId: 9606 ], 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)
C [auth A]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054845	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 [auth L]	C1-set_4	e1sy6L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set	e1sy6L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth H]	V-set_8	e1sy6H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B [auth H]	C1-set_1	e1sy6H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C [auth A]	I-set_4	e1sy6A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_4	ECOD (1.6)
C [auth A]	Ig_5	e1sy6A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ig_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth A]	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 [auth L]	OKT3 Fab, anti-CD3E / scCD3G-CD3E	L-KAPPA	Mus musculus (house mouse)	IGKV4-5901, IGKJ401, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202514-0)
B [auth H]	OKT3 Fab, anti-CD3E / scCD3G-CD3E	VH-CH1	Mus musculus (house mouse)	IGHV1-401, IGHJ201, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202514-0)
C [auth A]	scCD3G-CD3E	2C-LIKE	Homo sapiens (human)	CD3G*01	C-LIKE-DOMAIN C-LIKE	RPI	2C-LIKE	IMGT (202514-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L]	Light Chain	IGKV4	Kappa	t-cell surface glycoprotein cd3 gamma/epsilonchain	SAbDab (2025-04-18)
B [auth H]	Heavy Chain	IGHV1	-	t-cell surface glycoprotein cd3 gamma/epsilonchain	SAbDab (2025-04-18)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth L]	Muromonab	CD3E	Therapeutic SAbDab (2025-04-18)
B [auth H]	Muromonab	CD3E	Therapeutic SAbDab (2025-04-18)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	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 [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
C [auth A]	PF16680	T-cell surface glycoprotein CD3 delta chain (Ig_4)	T-cell surface glycoprotein CD3 delta chain	This is an immunoglobulin-like domain. It is found on the T-cell surface glycoprotein CD3 delta chain. CD3delta and CD3epsilon complex together as part of the T-cell receptor complex [1].	Domain
C [auth A]	PF16681	Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain (Ig_5)	Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain	Ig_5 is an immunoglobulin domain found on T-cell surface glycoprotein CD3 epsilon chain. It forms a first-order complex with T-cell surface glycoprotein CD3 delta chain as part of the T-cell receptor complex [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L]	OKT3 Fab light chain	-	-	-
B [auth H]	OKT3 Fab heavy chain	-	-	-
C [auth A]	T-cell surface glycoprotein CD3 gamma/epsilon chain	SH3 domain binding protein binding binding protein domain specific binding protein-containing complex binding signaling receptor binding T cell receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity kinase binding enzyme binding protein kinase binding SH3 domain binding protein binding binding protein domain specific binding protein-containing complex binding signaling receptor binding T cell receptor binding identical protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity kinase binding enzyme binding protein kinase binding signaling receptor complex adaptor activity protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of calcium-mediated signaling positive regulation of calcium-mediated signaling signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling regulation of cell communication cellular process positive regulation of signaling developmental process thymic T cell selection multicellular organismal process cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation negative thymic T cell selection anatomical structure development T cell differentiation negative T cell selection T cell selection leukocyte differentiation immune response adaptive immune response regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion positive regulation of cell-matrix adhesion cell adhesion cell-matrix adhesion positive regulation of cell-substrate adhesion regulation of cell-matrix adhesion regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process gamma-delta T cell activation regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death head development animal organ development brain development nervous system development multicellular organism development cerebellum development central nervous system development metencephalon development hindbrain development system development alpha-beta T cell activation immune system development regulation of T cell anergy lymphocyte anergy regulation of lymphocyte anergy positive regulation of lymphocyte anergy positive regulation of T cell tolerance induction positive regulation of T cell anergy regulation of immune system process regulation of multicellular organismal process regulation of T cell tolerance induction positive regulation of immune system process T cell anergy T cell tolerance induction positive regulation of multicellular organismal process regulation of tolerance induction positive regulation of tolerance induction tolerance induction positive regulation of cell population proliferation regulation of leukocyte activation regulation of alpha-beta T cell activation positive regulation of alpha-beta T cell proliferation regulation of cell activation positive regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of cell activation alpha-beta T cell proliferation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation regulation of CD4-positive, alpha-beta T cell proliferation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation positive regulation of alpha-beta T cell activation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion regulation of alpha-beta T cell proliferation positive regulation of lymphocyte activation positive regulation of CD4-positive, alpha-beta T cell activation cell-cell adhesion CD4-positive, alpha-beta T cell activation positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation CD4-positive, alpha-beta T cell proliferation regulation of T cell activation regulation of T cell proliferation regulation of CD4-positive, alpha-beta T cell activation regulation of mononuclear cell proliferation regulation of lymphocyte activation lymphocyte costimulation T cell costimulation protein-containing complex organization cellular component organization cellular component biogenesis signal complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis cell surface receptor signaling pathway smoothened signaling pathway immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response immune response-activating cell surface receptor signaling pathway T cell receptor signaling pathway regulation of immune response antigen receptor-mediated signaling pathway activation of immune response cell-cell adhesion mediated by integrin positive regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell-cell adhesion mediated by integrin positive regulation of cell-cell adhesion mediated by integrin cell adhesion mediated by integrin positive thymic T cell selection positive T cell selection negative regulation of signaling negative regulation of biological process negative regulation of cell communication negative regulation of smoothened signaling pathway negative regulation of cellular process regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction plasma membrane bounded cell projection organization cell projection organization neuron projection development generation of neurons neurogenesis neuron differentiation dendrite development neuron development regulation of cytokine production cytokine production regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production positive regulation of cytokine production cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway apoptotic signaling pathway G protein-coupled receptor signaling pathway negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of macromolecule metabolic process regulation of interleukin-4 production positive regulation of interleukin-4 production interleukin-4 production regulation of type II interferon production type II interferon production positive regulation of type II interferon production regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptidyl-tyrosine phosphorylation protein localization establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization regulation of leukocyte apoptotic process regulation of lymphocyte apoptotic process leukocyte apoptotic process lymphocyte apoptotic process establishment or maintenance of cell polarity	protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex T cell receptor complex cell surface external side of plasma membrane side of membrane protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex gamma-delta T cell receptor complex receptor complex cell periphery cellular anatomical structure plasma membrane signaling receptor complex T cell receptor complex cell surface external side of plasma membrane side of membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system alpha-beta T cell receptor complex neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree cell body immunological synapse endoplasmic reticulum intracellular vesicle 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 clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle membrane cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth H]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
C [auth A]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth A]	IPR015484	CD3 protein, epsilon/gamma/delta subunit	Family
C [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth A]	IPR003598	Immunoglobulin subtype 2	Domain
C [auth A]	IPR032052	CD3 gamma/delta subunit, Ig-like domain	Domain
C [auth A]	IPR015484	CD3 protein, epsilon/gamma/delta subunit	Family
C [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth A]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth A]	Pharos: P09693	immunodeficiency 18 severe combined immunodeficiency rheumatoid arthritis gastrointestinal stromal tumor primary immunodeficiency disease Inflammation lung carcinoma psoriasis lung adenocarcinoma malignant glioma non-small cell lung carcinoma glioblastoma lung cancer Omenn syndrome cutaneous lupus erythematosus immunodeficiency 18 severe combined immunodeficiency rheumatoid arthritis gastrointestinal stromal tumor primary immunodeficiency disease Inflammation lung carcinoma psoriasis lung adenocarcinoma malignant glioma non-small cell lung carcinoma glioblastoma lung cancer Omenn syndrome cutaneous lupus erythematosus MHC class II deficiency ovarian cancer combined immunodeficiency due to CD3gamma deficiency lung carcinoma interstitial cystitis Pre B-cell acute lymphoblastic leukemia cutaneous lupus erythematosus lung adenocarcinoma psoriasis IgA glomerulonephritis lung cancer osteosarcoma

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.