3F6Q | pdb_00003f6q

Crystal structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1 LIM1 domain

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3f6qa_	Alpha and beta proteins (a+b)	beta-hairpin-alpha-hairpin repeat	Ankyrin repeat	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)
A	SCOP2B Superfamily	Ankyrin repeat	8081107	3000154	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)
B	zf-CCCH_10	e3f6qB1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: zf-CCCH_10	ECOD (v294.1)
A	zf-CCCH_10	e3f6qA1	A: a/b three-layered sandwiches	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: zf-CCCH_10	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)
A	1.25.40.20	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Ankyrin repeat-containing domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00412	LIM domain (LIM)	LIM domain	This family represents two copies of the LIM structural domain.	Domain
A	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	LIM and senescent cell antigen-like-containing domain protein 1	protein binding binding kinase binding enzyme binding protein kinase binding cytoskeletal protein binding actin binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary 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 negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary 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 negative regulation of cellular process 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 biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cell adhesion cell-matrix adhesion cell-substrate adhesion cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling regulation of integrin-mediated signaling pathway positive regulation of integrin-mediated signaling pathway integrin-mediated signaling pathway cell surface receptor signaling pathway cellular response to endogenous stimulus cellular response to growth factor stimulus response to transforming growth factor beta cellular response to transforming growth factor beta stimulus response to endogenous stimulus response to growth factor response to cytokine cytokine-mediated signaling pathway response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus response to tumor necrosis factor cell-cell adhesion positive regulation of substrate adhesion-dependent cell spreading regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of cell-substrate adhesion substrate adhesion-dependent cell spreading cellular component organization cell junction organization cellular component organization or biogenesis cell-cell junction organization	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell-cell junction intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm cell periphery plasma membrane membrane
A	Integrin-linked protein kinase	protein-macromolecule adaptor activity molecular adaptor activity 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 protein-macromolecule adaptor activity molecular adaptor activity 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 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 protein binding signaling receptor binding cation binding magnesium ion binding metal ion binding cell adhesion molecule binding protein-containing complex binding integrin binding kinase binding enzyme binding protein kinase binding	developmental process multicellular organismal process cellular developmental process peripheral nervous system axon ensheathment peripheral nervous system development cell development nervous system development glial cell development myelination multicellular organism development neurogenesis Schwann cell development gliogenesis axon ensheathment ensheathment of neurons developmental process multicellular organismal process cellular developmental process peripheral nervous system axon ensheathment peripheral nervous system development cell development nervous system development glial cell development myelination multicellular organism development neurogenesis Schwann cell development gliogenesis axon ensheathment ensheathment of neurons glial cell differentiation cell differentiation anatomical structure development myelination in peripheral nervous system cellular process Schwann cell differentiation system development cell adhesion substrate adhesion-dependent cell spreading cell-substrate adhesion membrane organization membrane biogenesis membrane assembly plasma membrane raft organization cellular component organization cellular component biogenesis plasma membrane raft assembly caveola assembly cellular component assembly plasma membrane organization cellular component organization or biogenesis membrane raft organization membrane raft assembly endomembrane system organization regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis biological regulation platelet aggregation blood coagulation cell-cell adhesion response to stress coagulation regulation of biological quality response to wounding platelet activation ameboidal-type cell migration cell migration fibroblast migration cell motility positive regulation of substrate adhesion-dependent cell spreading regulation of biological process regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading regulation of cell adhesion positive regulation of biological process positive regulation of cell-substrate adhesion positive regulation of cellular process localization protein localization to cell periphery macromolecule localization intracellular protein localization protein localization to cell cortex anatomical structure morphogenesis cell morphogenesis cellular response to stimulus cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction response to tumor necrosis factor nerve development mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development renal system development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development animal organ morphogenesis epithelial tube morphogenesis nephron development nephron epithelium development ureteric bud development epithelium development tube development mesonephros development animal organ development morphogenesis of an epithelium tissue development tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis kidney development mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium cell-matrix adhesion positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling phosphatidylinositol 3-kinase/protein kinase B signal transduction integrin-mediated signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus regulation of transmembrane receptor protein serine/threonine kinase signaling pathway positive regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway response to BMP transforming growth factor beta receptor superfamily signaling pathway response to growth factor cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation neural precursor cell proliferation regulation of osteoblast differentiation regulation of developmental process regulation of cell differentiation osteoblast differentiation positive regulation of developmental process positive regulation of osteoblast differentiation ossification positive regulation of cell differentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process microtubule cytoskeleton organization mitotic cell cycle mitotic spindle organization organelle organization mitotic cell cycle process microtubule-based process cell cycle cytoskeleton organization microtubule cytoskeleton organization involved in mitosis spindle organization cell cycle process regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of canonical Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of cell population proliferation negative regulation of neural precursor cell proliferation negative regulation of biological process negative regulation of cellular process regulation of neural precursor cell proliferation cell projection organization establishment or maintenance of bipolar cell polarity establishment or maintenance of epithelial cell apical/basal polarity establishment or maintenance of apical/basal cell polarity establishment or maintenance of cell polarity heart development heart morphogenesis circulatory system development outflow tract morphogenesis	cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cell projection cellular anatomical structure cell leading edge plasma membrane bounded cell projection lamellipodium membrane intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cytoplasm cytosol chromatin chromosome sarcomere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex anchoring junction cell junction focal adhesion cell-substrate junction cell periphery cell cortex centrosome microtubule organizing center microtubule cytoskeleton plasma membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR047944	LIMS1/2-like, LIM domain 1	Domain
B	IPR017351	LIM and senescent cell antigen-like-containing domain protein 1-4-like	Family
B	IPR047946	LIM and senescent cell antigen-like-containing domain protein 1/2-like	Family
B	IPR001781	Zinc finger, LIM-type	Domain
A	IPR035692	Integrin-linked protein kinase, pseudokinase domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR002110	Ankyrin repeat	Repeat
A	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
A	IPR051681	Serine/Threonine Kinases and Pseudokinases	Family
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P48059	atypical teratoid rhabdoid tumor gastric carcinoma malignant pancreatic neoplasm pilocytic astrocytoma ulcerative colitis exocrine pancreatic carcinoma glioblastoma osteosarcoma psoriasis gastric cancer malignant glioma ovarian cancer tuberculosis
A	Pharos: Q13418	thoracic disease cocaine abuse Liver Cirrhosis, Experimental cocaine dependence epilepsy malignant mesothelioma transient ischemic attack polyp of colon dilated cardiomyopathy ovarian cancer rheumatoid arthritis osteosarcoma

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.