4NY0

Crystal structure of FERM domain of human focal adhesion kinase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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 D]	d4ny0d2	All alpha proteins	Acyl-CoA binding protein-like	Second domain of FERM	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth D]	d4ny0d3	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth D]	d4ny0d1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4ny0a2	All alpha proteins	Acyl-CoA binding protein-like	Second domain of FERM	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4ny0a3	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth A]	d4ny0a1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d4ny0b2	All alpha proteins	Acyl-CoA binding protein-like	Second domain of FERM	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d4ny0b3	All beta proteins	PH domain-like barrel	PH domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d4ny0b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth D]	FERM_C_FAK1	e4ny0D2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_FAK1	ECOD (1.6)
A [auth D]	FERM_M	e4ny0D3	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
A [auth D]	KOG4257	e4ny0D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4257	ECOD (1.6)
B [auth A]	FERM_C_FAK1	e4ny0A2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_FAK1	ECOD (1.6)
B [auth A]	FERM_M	e4ny0A3	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
B [auth A]	KOG4257	e4ny0A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4257	ECOD (1.6)
C [auth B]	FERM_C_FAK1	e4ny0B2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_FAK1	ECOD (1.6)
C [auth B]	FERM_M	e4ny0B3	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
C [auth B]	KOG4257	e4ny0B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4257	ECOD (1.6)
D [auth C]	FERM_C_FAK1	e4ny0C2	A: beta barrels	X: PH domain-like	H: PH domain-like (From Topology)	T: PH domain-like	F: FERM_C_FAK1	ECOD (1.6)
D [auth C]	FERM_M	e4ny0C3	A: alpha bundles	X: Acyl-CoA binding protein-like (From Topology)	H: Acyl-CoA binding protein-like (From Topology)	T: Acyl-CoA binding protein-like	F: FERM_M	ECOD (1.6)
D [auth C]	KOG4257	e4ny0C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KOG4257	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A [auth D]	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
A [auth D]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
B [auth A]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B [auth A]	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
B [auth A]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
C [auth B]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth B]	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
C [auth B]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)
D [auth C]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
D [auth C]	1.20.80.10	Mainly Alpha	Up-down Bundle	Acyl-CoA Binding Protein		CATH (4.3.0)
D [auth C]	2.30.29.30	Mainly Beta	Roll	PH-domain like	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth A], C [auth B], D [auth C]	PF21477	FAK1/PYK2, FERM domain C-lobe (FERM_C_FAK1)	FAK1/PYK2, FERM domain C-lobe	FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lo ...	FAK1 (focal adhesion kinase 1) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells and it is involved in diverse cellular roles. The N-terminal region of FAK1 contains a FERM domain which is subdivided FERM_N or A-lobe, FERM_M or B-lobe and FERM_C or C-lobe. This entry represents the C-lobe, which is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites [1-5]. This domain is also present in protein-tyrosine kinase 2-beta (also known as PYK2), a cytoplasmic, non-receptor tyrosine kinase which is a close paralogue to FAK in vertebrates. FRMPD1/3/4 also contain this domain; FRMPD1 regulates the subcellular location of activator of G-protein signaling 3 and its interaction with G-proteins. FRMPD4 has been shown to regulate dendritic spine morphogenesis and the function of FRMPD3 is not clear.	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	PF00373	FERM central domain (FERM_M)	FERM central domain	This domain is the central structural domain of the FERM domain.	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	PF18038	FERM N-terminal domain (FERM_N_2)	FERM N-terminal domain	This entry represents the FERM N-terminal domain found in focal adhesion kinases.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], B [auth A], C [auth B], D [auth C]	Focal adhesion kinase 1	protein phosphatase binding phosphatase binding protein binding binding enzyme 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 adenyl ribonucleotide binding protein phosphatase binding phosphatase binding protein binding binding enzyme 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 adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding non-membrane spanning protein tyrosine kinase activity JUN kinase binding kinase binding protein kinase binding SH2 domain binding protein domain specific binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity hydrolase activity, acting on ester bonds protein tyrosine phosphatase activity phosphatase activity hydrolase activity cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding cytoskeletal protein binding actin binding molecular function activator activity molecular function regulator activity	regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly positive regulation of response to wounding wound healing response to stimulus positive regulation of biological process regulation of response to wounding positive regulation of response to stimulus positive regulation of wound healing regulation of response to stimulus response to stress regulation of response to stress regulation of wound healing response to wounding developmental process placenta development animal organ development anatomical structure development regulation of cell motility endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration cell migration cell motility locomotion cellular response to stimulus 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 regulation of substrate adhesion-dependent cell spreading substrate adhesion-dependent cell spreading negative regulation of programmed cell death regulation of apoptotic process regulation of anoikis negative regulation of biological process regulation of programmed cell death cell death negative regulation of anoikis negative regulation of apoptotic process anoikis negative regulation of cellular process apoptotic process programmed cell death establishment of cell polarity establishment or maintenance of cell polarity negative regulation of cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion regulation of cell-cell adhesion protein phosphorylation protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process heart development multicellular organismal process heart morphogenesis circulatory system development multicellular organism development anatomical structure morphogenesis animal organ morphogenesis system development positive regulation of locomotion macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis positive regulation of macrophage migration regulation of leukocyte migration response to external stimulus positive regulation of leukocyte chemotaxis granulocyte migration leukocyte migration response to chemical regulation of response to external stimulus macrophage chemotaxis regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of response to external stimulus positive regulation of cell motility myeloid leukocyte migration positive regulation of mononuclear cell migration positive regulation of cellular process cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus immune system process granulocyte chemotaxis mononuclear cell migration positive regulation of macrophage chemotaxis leukocyte chemotaxis ERBB signaling pathway epidermal growth factor receptor signaling pathway cellular response to nitrogen compound response to peptide hormone cellular response to growth hormone stimulus cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus growth hormone receptor signaling pathway response to endogenous stimulus cellular response to peptide hormone stimulus response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound response to growth hormone detection of external stimulus detection of stimulus detection of mechanical stimulus detection of muscle stretch response to mechanical stimulus response to abiotic stimulus detection of abiotic stimulus response to muscle stretch regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process positive regulation of macromolecule metabolic process positive regulation of protein kinase activity positive regulation of protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process regulation of protein metabolic process positive regulation of catalytic activity regulation of cellular metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process epithelium migration tissue migration ameboidal-type cell migration regulation of multicellular organismal process epithelial cell migration regulation of epithelial cell migration regulation of hydrolase activity regulation of GTPase activity regulation of signaling protein-containing complex organization regulation of signal transduction signal complex assembly protein-containing complex assembly regulation of cell communication cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway regulation of osteoblast differentiation regulation of developmental process cellular developmental process regulation of cell differentiation osteoblast differentiation ossification cell differentiation netrin-activated signaling pathway cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition mesenchyme development positive regulation of developmental process positive regulation of cell differentiation tissue development epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation catabolic process proteolysis involved in protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis protein catabolic process regulation of catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process modification-dependent protein catabolic process positive regulation of proteolysis ubiquitin-dependent protein catabolic process regulation of fibroblast migration positive regulation of fibroblast migration fibroblast migration integrin-mediated signaling pathway positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette 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 regulation of cytoskeleton organization regulation of organelle organization organelle organization cytoskeleton organization regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation peptidyl-tyrosine modification peptidyl-amino acid modification peptidyl-tyrosine phosphorylation regulation of leukocyte proliferation leukocyte proliferation macrophage proliferation positive regulation of leukocyte proliferation positive regulation of macrophage proliferation regulation of macrophage proliferation axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron projection guidance neuron development vascular endothelial growth factor receptor signaling pathway immune response-regulating cell surface receptor signaling pathway involved in phagocytosis import into cell immune response-regulating cell surface receptor signaling pathway transport Fc-gamma receptor signaling pathway involved in phagocytosis vesicle-mediated transport localization immune response-activating signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway positive regulation of immune response phagocytosis Fc-gamma receptor signaling pathway immune response immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway establishment of localization immune effector process regulation of immune response endocytosis activation of immune response positive regulation of epithelial cell migration	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cellular anatomical entity cytosol intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle neuron spine synapse neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse cell junction dendrite dendritic tree actin filament bundle actin cytoskeleton actomyosin stress fiber contractile actin filament bundle perinuclear region of cytoplasm membrane-bounded organelle cilium ciliary basal body microtubule organizing center microtubule cytoskeleton anchoring junction focal adhesion cell-substrate junction cell periphery cell cortex centrosome plasma membrane membrane intracellular membrane-bounded organelle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], B [auth A], C [auth B], D [auth C]	IPR000299	FERM domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR041784	FAK1/PYK2, FERM domain C-lobe	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR008266	Tyrosine-protein kinase, active site	Active Site
A [auth D], B [auth A], C [auth B], D [auth C]	IPR019748	FERM central domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR000719	Protein kinase domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR041390	Focal adhesion kinase, N-terminal	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR035963	FERM superfamily, second domain	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR036137	Focal adhesion kinase, targeting (FAT) domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR017441	Protein kinase, ATP binding site	Binding Site
A [auth D], B [auth A], C [auth B], D [auth C]	IPR014352	FERM/acyl-CoA-binding protein superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR049385	FAK1-like, FERM domain C-lobe	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR011993	PH-like domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR019749	Band 4.1 domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B], D [auth C]	IPR005189	Focal adhesion kinase, targeting (FAT) domain	Domain
A [auth D], B [auth A], C [auth B], D [auth C]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth A], C [auth B], D [auth C]	Pharos: Q05397	squamous cell carcinoma rheumatoid arthritis glioblastoma non-small cell lung carcinoma atrial fibrillation giant cell glioblastoma Mammary Neoplasms, Experimental oral cavity neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida X-linked mixed deafness with perilymphatic gusher breast cancer hepatocellular carcinoma MALT lymphoma squamous cell carcinoma rheumatoid arthritis glioblastoma non-small cell lung carcinoma atrial fibrillation giant cell glioblastoma Mammary Neoplasms, Experimental oral cavity neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida X-linked mixed deafness with perilymphatic gusher breast cancer hepatocellular carcinoma MALT lymphoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma Pick disease breast disease oligodendroglioma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma attention deficit hyperactivity disorder, inattentive type cancer metastatic melanoma

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.