6KC4 | pdb_00006kc4

Crystal structure of human Fer SH2 domain bound to a phosphopeptide (DEpYENVD)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	SH2 domain	8067978	3000197	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	SH2 domain	8067978	3000197	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	SH2 domain	8067978	3000197	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	SH2 domain	8067978	3000197	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	SH2 domain	8067978	3000197	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	SH2 domain	8067978	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)
A	TSP_1	e6kc4A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Ntn	T: Proteasome subunits	F: TSP_1	ECOD (v294.1)
C	V-set	e6kc4C1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)
E	V-set	e6kc4E1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)
G	V-set	e6kc4G1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)
I	V-set	e6kc4I1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)
K	V-set	e6kc4K1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)
C	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)
E	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)
G	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)
I	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)
K	3.30.505.10	Alpha Beta	2-Layer Sandwich	SHC Adaptor Protein	SH2 domain	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00017	SH2 domain (SH2)	SH2 domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	phosphopeptide (EDpYENVD)	-	-	-
A, C, E, G, I A, C, E, G, I, K	Tyrosine-protein kinase Fer	protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding protein tyrosine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein phosphatase binding phosphatase binding protein phosphatase 1 binding protein binding enzyme binding non-membrane spanning protein tyrosine kinase activity lipid binding epidermal growth factor receptor binding signaling receptor binding growth factor receptor binding	cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of cellular process response to stimulus signaling peptidyl-tyrosine modification cell communication peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process signal transduction protein modification process phosphorus metabolic process tyrosine phosphorylation of STAT protein cellular response to stimulus cell surface receptor signaling pathway via STAT regulation of cellular process response to stimulus signaling peptidyl-tyrosine modification cell communication peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process signal transduction protein modification process phosphorus metabolic process tyrosine phosphorylation of STAT protein regulation of biological process protein phosphorylation cell surface receptor signaling pathway phosphorylation biological regulation primary metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT response to cytokine cytokine-mediated signaling pathway response to peptide response to chemical cellular response to cytokine stimulus response to macrophage colony-stimulating factor cellular response to macrophage colony-stimulating factor stimulus cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion response to endogenous stimulus response to growth factor response to platelet-derived growth factor cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization regulation of cell motility regulation of fibroblast migration fibroblast migration regulation of locomotion ameboidal-type cell migration regulation of cell migration cell migration cell motility locomotion protein autophosphorylation platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway chemotaxis taxis response to external stimulus regulation of ERBB signaling pathway regulation of signaling regulation of signal transduction regulation of epidermal growth factor receptor signaling pathway regulation of response to stimulus ERBB signaling pathway regulation of cell communication epidermal growth factor receptor signaling pathway multicellular organismal process regulation of immune effector process regulation of leukocyte activation negative regulation of biological process regulation of cell activation cell activation involved in immune response myeloid leukocyte activation leukocyte activation leukocyte activation involved in immune response negative regulation of cellular process mast cell activation regulation of immune system process regulation of mast cell activation regulation of multicellular organismal process immune response negative regulation of response to stimulus negative regulation of immune response cell activation negative regulation of immune effector process myeloid cell activation involved in immune response immune effector process negative regulation of cell activation negative regulation of mast cell activation mast cell activation involved in immune response negative regulation of immune system process negative regulation of mast cell activation involved in immune response immune system process regulation of immune response negative regulation of multicellular organismal process negative regulation of leukocyte activation immune response-regulating cell surface receptor signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway Fc-epsilon receptor signaling pathway cellular response to stem cell factor stimulus Kit signaling pathway response to stem cell factor adherens junction organization cellular component disassembly cell junction organization cell junction disassembly cell-cell junction disassembly adherens junction disassembly cell-cell junction organization cellular developmental process reproductive process sex differentiation cell development developmental process involved in reproduction epithelial cell differentiation Sertoli cell differentiation male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics cell differentiation anatomical structure development reproductive structure development system development developmental process epithelium development gonad development reproductive system development Sertoli cell development animal organ development tissue development epithelial cell development adherens junction assembly cellular component biogenesis cellular component assembly cell junction assembly cell-cell junction assembly tube development seminiferous tubule development sexual reproduction multicellular organismal reproductive process cellular process involved in reproduction in multicellular organism gamete generation germ cell development leukocyte migration diapedesis cellular extravasation positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling cell-cell adhesion cell-cell adhesion mediated by cadherin cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation interleukin-6-mediated signaling pathway response to interleukin-6 cellular response to interleukin-6 cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus cellular response to peptide hormone stimulus response to nitrogen compound 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 regulation of protein-containing complex assembly positive regulation of protein-containing complex 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 positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility extracellular matrix-cell signaling microtubule cytoskeleton organization microtubule-based process regulation of protein modification process regulation of protein phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization regulation of cell projection organization regulation of cell projection assembly plasma membrane bounded cell projection assembly regulation of plasma membrane bounded cell projection assembly regulation of lamellipodium assembly regulation of lamellipodium organization lamellipodium organization regulation of plasma membrane bounded cell projection organization cell projection assembly biological process involved in interspecies interaction between organisms response to lipid response to other organism response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome cell-cell junction adherens junction anchoring junction cell junction cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome cell-cell junction adherens junction anchoring junction cell junction cytoskeleton cell periphery cell cortex plasma membrane membrane protein-containing complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane cell projection membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR008266	Tyrosine-protein kinase, active site	Active Site
A, C, E, G, I A, C, E, G, I, K	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR037452	Tyrosine-protein kinase Fer, F-BAR domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR000719	Protein kinase domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR031160	F-BAR domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR001060	FCH domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR017441	Protein kinase, ATP binding site	Binding Site
A, C, E, G, I A, C, E, G, I, K	IPR036860	SH2 domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR000980	SH2 domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR016250	Tyrosine-protein kinase, Fes/Fps type	Family
A, C, E, G, I A, C, E, G, I, K	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR050198	Non-receptor tyrosine kinases involved in cell signaling	Family
A, C, E, G, I A, C, E, G, I, K	IPR035849	Fes/Fps/Fer, SH2 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G, I A, C, E, G, I, K	Pharos: P16591	ALK fusion gene-positive non-small-cell lung cancer invasive ductal breast carcinoma osteosarcoma cancer lung adenocarcinoma ovarian cancer diabetes mellitus non-small cell lung carcinoma ovarian endometrioid adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, 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.