5QU4 | pdb_00005qu4

Crystal Structure of swapped human Nck SH3.1 domain, 1.05A, orthorhombic form I

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D	d5qu4d_	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5qu4c_	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5qu4b1	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5qu4b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5qu4a_	All beta proteins	SH3-like barrel	SH3-domain	automated matches	automated matches	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)
D	SCOP2B Superfamily	SH3-domain	8065169	3000153	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH3-domain	8065169	3000153	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	SH3-domain	8065169	3000153	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SH3-domain	8065169	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)
D	Chlor_dismutase	e5qu4D1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (v294.1)
C	Chlor_dismutase	e5qu4C1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (v294.1)
B	V-set	e5qu4B1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: V-set	ECOD (v294.1)
A	Chlor_dismutase	e5qu4A1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: beta-sandwich domain in metalloprotease stcE	F: Chlor_dismutase	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00018	SH3 domain (SH3_1)	SH3 domain	SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase Swiss:P12931. The structure is a partly opened beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Cytoplasmic protein NCK1	protein binding binding eukaryotic initiation factor eIF2 binding translation initiation factor binding protein-macromolecule adaptor activity molecular adaptor activity cell adhesion molecule binding cadherin binding signaling receptor binding ephrin receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein binding binding eukaryotic initiation factor eIF2 binding translation initiation factor binding protein-macromolecule adaptor activity molecular adaptor activity cell adhesion molecule binding cadherin binding signaling receptor binding ephrin receptor binding protein tyrosine kinase binding kinase binding receptor tyrosine kinase binding enzyme binding protein kinase binding protein domain specific binding enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity kinase inhibitor activity kinase regulator activity signaling adaptor activity molecular condensate scaffold activity molecular sequestering activity protein sequestering activity cytoskeletal anchor activity signaling receptor complex adaptor activity	cellular response to stimulus regulation of cellular process response to stimulus positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translation in response to stress cellular response to stress positive regulation of biosynthetic process response to stress cellular response to stimulus regulation of cellular process response to stimulus positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translation in response to stress cellular response to stress positive regulation of biosynthetic process response to stress positive regulation of macromolecule metabolic process protein metabolic process positive regulation of translation in response to stress positive regulation of cellular process response to endoplasmic reticulum stress positive regulation of translation in response to endoplasmic reticulum stress regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of translation in response to endoplasmic reticulum stress biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic 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 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 regulation of cell motility regulation of locomotion regulation of cell migration locomotion cellular response to nitrogen compound negative regulation of signaling response to peptide hormone negative regulation of biological process regulation of signal transduction insulin receptor signaling pathway regulation of cellular response to insulin stimulus negative regulation of cell communication cellular response to endogenous stimulus response to hormone negative regulation of cellular process cellular response to hormone stimulus regulation of signaling negative regulation of response to stimulus response to endogenous stimulus regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound negative regulation of signal transduction cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of cellular response to insulin stimulus regulation of response to stimulus negative regulation of insulin receptor signaling pathway response to chemical response to insulin regulation of cell communication cellular response to insulin stimulus regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization immune response-regulating cell surface receptor signaling pathway regulation of antigen receptor-mediated signaling pathway negative regulation of antigen receptor-mediated signaling pathway positive regulation of response to stimulus 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 regulation of T cell receptor signaling pathway T cell receptor signaling pathway negative regulation of T cell receptor signaling pathway negative regulation of immune system process immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process 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 RNA biosynthetic process negative regulation of macromolecule 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 metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process protein-containing complex organization signal complex assembly protein-containing complex assembly organelle organization actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization cytoskeleton organization positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population 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 lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation 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 cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process translational initiation regulation of translational initiation regulation of translation initiation in response to endoplasmic reticulum stress regulation of translational initiation in response to stress regulation of cap-independent translational initiation positive regulation of cap-independent translational initiation cap-independent translational initiation positive regulation of cytoplasmic translational initiation regulation of cytoplasmic translational initiation cytoplasmic translation cytoplasmic translational initiation positive regulation of translational initiation regulation of cytoplasmic translation substrate-dependent cell migration, cell extension substrate-dependent cell migration positive regulation of cap-dependent translational initiation cap-dependent translational initiation regulation of cap-dependent translational initiation 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 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 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 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 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 biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism innate immune response antiviral innate immune response response to external biotic stimulus response to virus positive regulation of organelle organization regulation of cytoskeleton 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 regulation of actin filament polymerization regulation of biological quality protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin filament polymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization 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 positive regulation of actin filament polymerization regulation of anatomical structure size negative regulation of intracellular signal transduction PERK-mediated unfolded protein response endoplasmic reticulum unfolded protein response integrated stress response signaling regulation of endoplasmic reticulum unfolded protein response intracellular signaling cassette ER-nucleus signaling pathway 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 cellular response to unfolded protein response to unfolded protein negative regulation of PERK-mediated unfolded protein response response to topologically incorrect protein	cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle vesicle membrane organelle membrane vesicle organelle membrane phosphatase complex cell-cell junction cellular anatomical structure anchoring junction cell junction intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle vesicle membrane organelle membrane vesicle organelle membrane phosphatase complex protein-containing complex protein phosphatase type 1 complex catalytic complex protein serine/threonine phosphatase complex cell periphery plasma membrane intracellular organelle membraneless organelle intracellular membraneless organelle ribosome nucleus intracellular membrane-bounded organelle endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR035564	Nck1, SH3 domain 2	Domain
A, B, C, D	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR035562	Nck1, SH3 domain 1	Domain
A, B, C, D	IPR001452	SH3 domain	Domain
A, B, C, D	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, B, C, D	IPR035882	Nck1, SH2 domain	Domain
A, B, C, D	IPR000980	SH2 domain	Domain
A, B, C, D	IPR035565	Nck1, SH3 domain 3	Domain
A, B, C, D	IPR051184	Tyrosine-phosphorylated adapter molecule	Family
A, B, C, D	IPR017304	Cytoplasmic protein NCK	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P16333	nephrotic syndrome Albuminuria proteinuria lung cancer ovarian cancer Sjogren syndrome astrocytic tumor tuberculosis endogenous depression osteosarcoma psoriasis

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.