2DM5 | pdb_00002dm5

Thermodynamic Penalty Arising From Burial of a Ligand Polar Group Within a Hydrophobic Pocket of a Protein Receptor

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2dm5a_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	Major urinary protein/alpha-2u-globulin	house mouse (Mus musculus ) [TaxId: 10090 ],	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	Lipocalin	e2dm5A1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Major Urinary Protein	molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity protein-hormone receptor activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity insulin receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity protein-hormone receptor activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity insulin receptor activity catalytic activity pheromone binding binding odorant 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 regulation of lipid metabolic process lipid biosynthetic process negative regulation of lipid biosynthetic process regulation of lipid biosynthetic process negative regulation of lipid metabolic process lipid metabolic process aerobic respiration cellular respiration energy derivation by oxidation of organic compounds generation of precursor metabolites and energy positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of lipid metabolic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process positive regulation of glucose metabolic process regulation of small molecule metabolic process small molecule metabolic process positive regulation of carbohydrate metabolic process positive regulation of small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process cellular response to stimulus positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction response to stimulus signaling 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 regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling energy reserve metabolic process regulation of localization lipid storage lipid localization negative regulation of lipid localization localization regulation of lipid storage regulation of lipid localization negative regulation of lipid storage macromolecule localization nutrient storage protein localization negative regulation of protein transport establishment of protein localization nitrogen compound transport negative regulation of transport negative regulation of secretion carbohydrate homeostasis cellular macromolecule localization establishment of localization in cell negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization intracellular glucose homeostasis protein secretion establishment of localization cellular response to oxygen-containing compound regulation of protein secretion regulation of secretion cellular response to carbohydrate stimulus chemical homeostasis negative regulation of protein secretion response to glucose response to chemical glucose homeostasis insulin secretion involved in cellular response to glucose stimulus cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion transport homeostatic process negative regulation of signaling hormone secretion negative regulation of cell communication protein localization to extracellular region negative regulation of peptide secretion peptide secretion regulation of secretion by cell secretion by cell response to monosaccharide response to carbohydrate amide transport signal release cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus negative regulation of protein localization regulation of transport secretion negative regulation of response to stimulus regulation of peptide transport negative regulation of insulin secretion involved in cellular response to glucose stimulus regulation of establishment of protein localization export from cell cell-cell signaling response to oxygen-containing compound cellular response to glucose stimulus regulation of protein transport peptide transport response to hexose cellular response to chemical stimulus cellular homeostasis negative regulation of insulin secretion protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion regulation of insulin secretion involved in cellular response to glucose stimulus hormone transport insulin secretion behavior rhythmic process multicellular organismal process circadian behavior locomotory behavior rhythmic behavior circadian rhythm locomotor rhythm negative regulation of small molecule metabolic process gluconeogenesis negative regulation of gluconeogenesis negative regulation of carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide biosynthetic process hexose biosynthetic process regulation of gluconeogenesis regulation of carbohydrate biosynthetic process cellular component organization organelle organization cellular component organization or biogenesis mitochondrion organization multicellular organismal-level homeostasis temperature homeostasis heat generation response to lipid cellular response to lipid	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region extracellular space membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012674	Calycin	Homologous Superfamily
A	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A	IPR022272	Lipocalin family conserved site	Conserved Site
A	IPR002971	Major urinary protein	Family
A	IPR002345	Lipocalin	Family

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.