3N84 | pdb_00003n84

Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d3n84f_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3n84e1	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3n84e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3n84d_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3n84c_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3n84b_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3n84a_	Alpha and beta proteins (a+b)	SH2-like	SH2 domain	SH2 domain	Growth factor receptor-bound protein 2 (GRB2)	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)
F	SCOP2B Superfamily	SH2 domain	8040052	3000197	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SH2 domain	8040052	3000197	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	SH2 domain	8040052	3000197	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH2 domain	8040052	3000197	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH2 domain	8040052	3000197	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH2 domain	8040052	3000197	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	Gal-bind_lectin	e3n84F1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
E	Gal-bind_lectin	e3n84E1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
D	Gal-bind_lectin	e3n84D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
C	Gal-bind_lectin	e3n84C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
B	Gal-bind_lectin	e3n84B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)
A	Gal-bind_lectin	e3n84A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Gal-bind_lectin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
E	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
D	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
C	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
B	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00017	SH2 domain (SH2)	SH2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	23-membered peptide-like macrocyclic ligand	-	-	-
A, B, C, D, E A, B, C, D, E, F	Growth factor receptor-bound protein 2	protein binding binding insulin receptor substrate binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor adaptor activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein-macromolecule adaptor activity molecular adaptor activity phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding protein phosphatase binding protein binding binding insulin receptor substrate binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor adaptor activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein-macromolecule adaptor activity molecular adaptor activity phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding protein phosphatase binding phosphatase binding enzyme binding neurotrophin TRK receptor binding neurotrophin TRKA receptor binding signaling receptor binding cytokine receptor binding neurotrophin receptor binding SH3 domain binding protein domain specific binding ephrin receptor binding identical protein binding transmembrane receptor protein tyrosine kinase adaptor activity protein tyrosine kinase binding receptor tyrosine kinase binding protein kinase binding signaling adaptor activity signaling receptor complex adaptor activity kinase binding RNA binding nucleic acid binding epidermal growth factor receptor binding growth factor receptor binding	localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus localization import into cell receptor internalization transport cellular process receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process regulation of signaling regulation of cellular process response to stimulus signaling biological regulation regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication signal transduction response to ionizing radiation cellular response to ionizing radiation response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus negative regulation of signaling negative regulation of ERBB signaling pathway negative regulation of biological process cell surface receptor protein tyrosine kinase signaling pathway negative regulation of cell communication regulation of epidermal growth factor receptor signaling pathway negative regulation of cellular process epidermal growth factor receptor signaling pathway enzyme-linked receptor protein signaling pathway regulation of ERBB signaling pathway cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of epidermal growth factor receptor signaling pathway ERBB signaling pathway cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization multicellular organismal process chordate embryonic development labyrinthine layer development embryo development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching anatomical structure development embryonic organ development developmental process epithelium development placenta development embryonic morphogenesis animal organ development morphogenesis of an epithelium branching involved in labyrinthine layer morphogenesis tissue development in utero embryonic development embryonic placenta morphogenesis anatomical structure morphogenesis labyrinthine layer morphogenesis tissue morphogenesis morphogenesis of a branching structure morphogenesis of a branching epithelium insulin-like growth factor receptor signaling pathway positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction regulation of small GTPase mediated signal transduction positive regulation of biological process positive regulation of response to stimulus positive regulation of cellular process Rac protein signal transduction positive regulation of intracellular signal transduction regulation of Rac protein signal transduction positive regulation of Rac protein signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of signaling immune response-regulating cell surface receptor signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response cellular response to stress DNA damage response response to stress signal transduction in response to DNA damage formation of primary germ layer cellular developmental process gastrulation endoderm development cell differentiation anatomical structure formation involved in morphogenesis endoderm formation endodermal cell differentiation peripheral nervous system development cell development nervous system development glial cell development neurogenesis Schwann cell development gliogenesis glial cell differentiation Schwann cell differentiation system development regulation of immune effector process lymphocyte mediated immunity negative regulation of lymphocyte mediated immunity response to biotic stimulus negative regulation of natural killer cell mediated immunity leukocyte mediated immunity natural killer cell mediated immunity regulation of natural killer cell mediated immunity response to other organism regulation of innate immune response negative regulation of immune response negative regulation of immune effector process response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity defense response to other organism negative regulation of response to external stimulus negative regulation of defense response natural killer cell mediated cytotoxicity regulation of cell killing negative regulation of natural killer cell mediated cytotoxicity regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus regulation of response to stress negative regulation of leukocyte mediated cytotoxicity innate immune response response to external biotic stimulus negative regulation of cell killing defense response regulation of leukocyte mediated cytotoxicity defense response to symbiont regulation of lymphocyte mediated immunity negative regulation of immune system process negative regulation of leukocyte mediated immunity cell killing negative regulation of innate immune response reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process metabolic process regulation of metabolic process regulation of reactive oxygen species metabolic process Ras protein signal transduction T cell activation cell activation lymphocyte activation leukocyte activation response to fibroblast growth factor cellular response to growth factor stimulus response to endogenous stimulus cellular response to endogenous stimulus fibroblast growth factor receptor signaling pathway response to growth factor cellular response to fibroblast growth factor stimulus cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway response to hormone cellular response to hormone stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin cellular response to insulin stimulus positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of actin filament-based process positive regulation of cellular component organization regulation of cellular component size cellular component biogenesis regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of protein polymerization protein-containing complex assembly regulation of actin filament polymerization regulation of biological quality protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization regulation of anatomical structure size myelination axon ensheathment ensheathment of neurons	cell-cell junction cellular anatomical structure anchoring junction cell junction cell periphery protein-containing complex Grb2-EGFR complex plasma membrane protein complex membrane plasma membrane membrane protein complex extracellular exosome membrane-bounded organelle extracellular vesicle cell-cell junction cellular anatomical structure anchoring junction cell junction cell periphery protein-containing complex Grb2-EGFR complex plasma membrane protein complex membrane plasma membrane membrane protein complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol intracellular organelle nucleus nuclear protein-containing complex COP9 signalosome intracellular membrane-bounded organelle vesicle membrane organelle membrane Golgi apparatus endomembrane system cell cortex centrosome microtubule organizing center cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen endosome intracellular vesicle cytoplasmic vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001452	SH3 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR035643	GRB2, C-terminal SH3 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR035641	GRB2, N-terminal SH3 domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR043539	Grb2-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000980	SH2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P62993	cancer large cell medulloblastoma ovarian cancer schizophrenia systemic sclerosis invasive ductal breast carcinoma non-alcoholic fatty liver disease psoriasis speech-language disorder-1 juvenile dermatomyositis osteosarcoma rheumatoid arthritis systemic lupus erythematosus

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K G, H, I, J, K, L	011
G, H, I, J, K G, H, I, J, K, L	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

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.