2CO8

Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains

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	d2co8a1	Small proteins	Glucocorticoid receptor-like (DNA-binding domain)	Glucocorticoid receptor-like (DNA-binding domain)	LIM domain	Nedd9 interacting protein with calponin homology, NICAL (MICAL1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2co8a4	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2co8a3	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	SCOP2 Family	LIM domain	8026746	4003634	SCOP2 (2022-06-29)
A	SCOP2 Family	LIM domain	8026749	4003634	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039125	3000068	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8039128	3000068	SCOP2 (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	F_UNCLASSIFIED	e2co8A2	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.110.10	Mainly Beta	Ribbon	Cysteine Rich Protein	Cysteine Rich Protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00412	LIM domain (LIM)	LIM domain	This family represents two copies of the LIM structural domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	NEDD9 interacting protein with calponin homology and LIM domains	small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding NAD(P)H oxidase H2O2-forming activity oxidoreductase activity NADPH oxidase H202-forming activity oxidoreductase activity, acting on NAD(P)H catalytic activity small GTPase binding protein binding binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding NAD(P)H oxidase H2O2-forming activity oxidoreductase activity NADPH oxidase H202-forming activity oxidoreductase activity, acting on NAD(P)H catalytic activity oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor FAD binding flavin adenine dinucleotide binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding monooxygenase activity SH3 domain binding protein domain specific binding kinase binding protein kinase binding oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen cation binding metal ion binding	cellular metabolic process sulfur compound metabolic process metabolic process cellular process sulfur oxidation regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process cellular metabolic process sulfur compound metabolic process metabolic process cellular process sulfur oxidation regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process negative regulation of phosphorylation regulation of metabolic process cellular component disassembly actin polymerization or depolymerization actin cytoskeleton organization protein-containing complex organization actin filament organization protein-containing complex disassembly actin filament depolymerization cellular component organization organelle organization actin filament-based process cellular component organization or biogenesis supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of localization regulated exocytosis transport secretion regulation of transport export from cell regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport regulation of secretion regulation of regulated secretory pathway localization secretion by cell regulation of secretion by cell exocytosis regulation of exocytosis cellular response to stimulus response to stimulus signaling signal transduction cell communication cellular component biogenesis cellular component assembly actin filament bundle organization actin filament bundle assembly	midbody cellular anatomical entity polymeric cytoskeletal fiber intracellular anatomical structure intermediate filament cytoskeleton intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle midbody cellular anatomical entity polymeric cytoskeletal fiber intracellular anatomical structure intermediate filament cytoskeleton intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle intermediate filament supramolecular fiber supramolecular polymer supramolecular complex non-membrane-bounded organelle actin cytoskeleton cytoplasm cytosol cell periphery plasma membrane membrane axon synapse hippocampal mossy fiber expansion neuron projection axon terminus plasma membrane bounded cell projection hippocampal mossy fiber presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus intercellular bridge endosome membrane membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane actin filament

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR001715	Calponin homology domain	Domain
A	IPR002938	FAD-binding domain	Domain
A	IPR022735	bMERB domain	Domain
A	IPR001781	Zinc finger, LIM-type	Domain
A	IPR036872	CH domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q8TDZ2	Autosomal dominant epilepsy with auditory features Malignant neoplasm of breast oligodendroglioma pancreatic ductal adenocarcinoma Pick disease gastric carcinoma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma spina bifida malignant mesothelioma non-small cell lung carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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 R01GM133198.