4E6R

Crystal structure of a Cytoplasmic protein NCK2 (NCK2) from Homo sapiens at 2.20 A resolution

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4e6ra1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4e6ra2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4e6rb1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4e6rb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	SH3-domain	8090158	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8090158	3000153	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	SH3_1	e4e6rA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)
B	SH3_1	e4e6rB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: SH3_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)
B	2.30.30.40	Mainly Beta	Roll	SH3 type barrels.	SH3 Domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14604	Variant SH3 domain (SH3_9)	Variant SH3 domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cytoplasmic protein NCK2	protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity scaffold protein binding protein binding binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding protein-containing complex binding cytoskeletal anchor activity protein tyrosine kinase binding kinase binding signaling receptor binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity scaffold protein binding protein binding binding phosphoprotein binding phosphotyrosine residue binding protein phosphorylated amino acid binding protein-containing complex binding cytoskeletal anchor activity protein tyrosine kinase binding kinase binding signaling receptor binding receptor tyrosine kinase binding enzyme binding protein kinase binding signaling receptor complex adaptor activity	cellular response to stimulus regulation of cellular process response to stimulus organonitrogen compound biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of translation in response to stress response to endoplasmic reticulum stress positive regulation of translation in response to endoplasmic reticulum stress regulation of biological process cellular response to stimulus regulation of cellular process response to stimulus organonitrogen compound biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of translation in response to stress response to endoplasmic reticulum stress positive regulation of translation in response to endoplasmic reticulum stress regulation of biological process cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process cellular biosynthetic process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of cellular metabolic process regulation of translation in response to stress organic substance metabolic process cellular response to stress positive regulation of biosynthetic process response to stress protein metabolic process positive regulation of cellular process regulation of biosynthetic process organonitrogen compound metabolic process regulation of translation in response to endoplasmic reticulum stress biological regulation regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process positive regulation of gene expression regulation of translation cellular process positive regulation of cellular biosynthetic process lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly cellular component organization cellular component biogenesis cellular component assembly lamellipodium organization cellular component organization or biogenesis cell projection assembly protein dephosphorylation regulation of protein modification process peptidyl-serine dephosphorylation positive regulation of phosphate metabolic process positive regulation of protein modification process positive regulation of peptidyl-serine dephosphorylation regulation of phosphate metabolic process phosphate-containing compound metabolic process protein modification process phosphorus metabolic process positive regulation of phosphorus metabolic process positive regulation of dephosphorylation regulation of dephosphorylation regulation of protein dephosphorylation dephosphorylation positive regulation of protein dephosphorylation regulation of peptidyl-serine dephosphorylation macromolecule modification regulation of phosphorus metabolic process cell surface receptor signaling pathway signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction enzyme-linked receptor protein signaling pathway ephrin receptor signaling pathway cell migration cell motility positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress regulation of response to endoplasmic reticulum stress regulation of signal transduction regulation of programmed cell death intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress regulation of intrinsic apoptotic signaling pathway intracellular signal transduction positive regulation of apoptotic signaling pathway positive regulation of response to stimulus regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway positive regulation of response to endoplasmic reticulum stress regulation of intracellular signal transduction regulation of response to stress intrinsic apoptotic signaling pathway regulation of signaling positive regulation of programmed cell death regulation of apoptotic process positive regulation of intracellular signal transduction cell death positive regulation of apoptotic process apoptotic signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of intrinsic apoptotic signaling pathway positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway positive regulation of signaling multicellular organismal process T cell activation immune system process cell activation lymphocyte activation leukocyte activation ERBB signaling pathway epidermal growth factor receptor signaling pathway positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization positive regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization protein-containing complex assembly actin filament-based process regulation of actin filament polymerization regulation of biological quality protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization actin cytoskeleton organization protein-containing complex organization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization actin filament organization regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of cellular component biogenesis regulation of organelle organization 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 cytoskeleton organization regulation of anatomical structure size developmental process dendritic spine development cellular developmental process cell development neuron projection development nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation dendrite development cell differentiation neuron development anatomical structure development system development negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process immunological synapse formation cell-cell recognition cell recognition regulation of translational initiation by eIF2 alpha phosphorylation negative regulation of cellular metabolic process negative regulation of protein modification process translational initiation negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of translational initiation regulation of translation initiation in response to endoplasmic reticulum stress negative regulation of metabolic process eiF2alpha phosphorylation in response to endoplasmic reticulum stress negative regulation of protein phosphorylation regulation of protein phosphorylation negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation negative regulation of phosphate metabolic process negative regulation of macromolecule metabolic process negative regulation of phosphorus metabolic process regulation of translational initiation in response to stress regulation of phosphorylation negative regulation of phosphorylation response to organic substance negative regulation of signaling negative regulation of intracellular signal transduction PERK-mediated unfolded protein response endoplasmic reticulum unfolded protein response integrated stress response signaling negative regulation of cell communication regulation of endoplasmic reticulum unfolded protein response intracellular signaling cassette ER-nucleus signaling pathway cellular response to organic substance negative regulation of endoplasmic reticulum unfolded protein response negative regulation of response to endoplasmic reticulum stress cellular response to topologically incorrect protein regulation of PERK-mediated unfolded protein response negative regulation of response to stimulus cellular response to unfolded protein response to unfolded protein negative regulation of signal transduction negative regulation of PERK-mediated unfolded protein response cellular response to chemical stimulus response to chemical response to topologically incorrect protein negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of cellular biosynthetic process organic cyclic compound metabolic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process signal complex assembly positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of immune system process positive regulation of immune system process regulation of leukocyte proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of multicellular organismal process positive regulation of leukocyte cell-cell adhesion leukocyte proliferation leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of RNA biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle vesicle membrane organelle membrane vesicle organelle membrane postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle vesicle membrane organelle membrane vesicle organelle membrane postsynaptic density postsynapse neuron to neuron synapse postsynaptic specialization synapse cell junction asymmetric synapse intracellular organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035559	Nck2, SH3 domain 1	Domain
A, B	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B	IPR035560	Nck2, SH3 domain 2	Domain
A, B	IPR000980	SH2 domain	Domain
A, B	IPR035883	Nck2, SH2 domain	Domain
A, B	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B	IPR035561	Nck2, SH3 domain 3	Domain
A, B	IPR001452	SH3 domain	Domain
A, B	IPR017304	Cytoplasmic protein NCK	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O43639	nephrotic syndrome Albuminuria proteinuria breast cancer osteosarcoma glioblastoma ovarian cancer

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B	DMG	RESID: AA0620 PSI-MOD : N,N-dimethylglycine MOD:01983
A, B	MLY	Parent Component: LYS RESID: AA0620 , AA0075 PSI-MOD : N,N-dimethylglycine MOD:01983 , N6,N6-dimethyl-L-lysine MOD:00084
A, B	MSE	Parent Component: MET RESID: AA0620 , AA0075

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.