Sub Concept defining structure of the Turn present in a Protein Concept for definition of a Protein Complex About Protein Complex Concept. A protein complex is a group of associated proteins. Protein complexes are a form of quaternary structure. Understanding the functional interactions of proteins is an important research focus in biochemistry, often referred to as proteomics. Sub Concept defining Monogenetic and Polygenetic defects present in the Protein Complex Concept defining Protein Entry About Derived Concept of Entry Describes the experiment and the biological macromolecules present in the entry. Specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. Sub Concept defining Biological Functions of the Protein Sub Concept defining Pathological Functions of the Protein About Derived Concept of Structural Domains The secondary structure details of a protein. It describes helices, sheets, and turns found in protein and polypeptide structures. Complex Concept defining Structural Folds and Domains present in Protein Structure. Specify salt bridges in the protein. Sub Concept defining Source Cell of the Protein Specifies the biological and/or chemical source of each biological molecule in the entry. Sources are described by both the common name and the scientific name, e.g., genus and species. Strain and/or cell-line for immortalized cells are given when they help to uniquely identify the biological entity studied. Sub Concept defining Water Solubility of Protein Atom records in protein databases present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. About Generic Concept of Atoms. Generic Concept defining 3D Protein Structure Atoms About Generic Concept of AtomicBind. Identify and describe each of the two atoms involved in the hydrogen bonds, residue links and salt bridges found in protein and polypeptide structures. Generic Concept for Bindings of Bonds like: Hydrogen Bond, Residue Links, Salt Bridges Sub Concept containing All Sheets present in Protein Specify the existence and location of disulfide bonds and other linkages. Generic Concept defining Residues in the Protein About Generic Concept of Residues. Residue refers to a portion of a larger molecule; for example in biochemistry, a residue refers to a specific monomer of a polysaccharide, protein, nucleic acid. In context of Protein Ontology residue represents one of the 20 amino acids that build protein sequence represnted by a three-alphabet code like: CYS. Sub Concept describing Protein Entry Sub Concept defining a specific Sheet present in a Protein Complex Concept defining Peptides found in Protein's cis configuration Sub Concept defining structure of the Helix present in a Protein Identify turns and other short loop turns which normally connect other secondary structure segments. Complex Concept defining the Constraints affecting Final Protein Conformation. Gentetic and environmental factors affecting final protein structure. About Derived Concept of Constraints Annotation Sub Concept defining Modified Residues present in Protein Helix identifies the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length. Complex Concept defining Protein Structure of the Protein Contains the collection of atomic coordinates and describes the geometry of the crystallographic experiment and the coordinate system transformations. About Derived Concept of Structure Complex Concept defining Functional Classification Domains of the Protein. About Derived Concept of Functional Domains First Functional Domain Classification Model based on biological functionality of protein in a cell Chains in Protein Ontology describe the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied. About Generric Concepts of Chains. Generic Concept defining Chains of Residue Sequences Allows to specify the existence and location of disulfide bonds and other linkages. About Derived Concept of Chemical Bonds Complex Concept defining Chemical Bonds present in Protein About Protein Ontology Concept. Protein Ontology contains concepts from general to specific and their properties categorized as data type property, object type property, reference type property, and annotation type property, which are data descriptors for protein data. Root Concept of Protein Ontology Generic Concept defining Protein Family A protein family is a group of evolutionarily related proteins. Superfamily is a group of protein families. About Generic Concept of Family. Sub Concept containing All Helices present in a Protein Sub Concept defining Physiological Functions of the Protein Sub Concept defining Literature References of Protein Specify hydrogen bonds in the protein. Sub Concept describing Crystallographic Details of Protein Structure About Generic Concept of Bind. Identify and describe each of the two residues involved in the disulfide bonds, prolines and other peptides found to be in the cis conformation in protein and polypeptide structures. Generic Concept for Bindings of Bonds like: Disulphide Bond, CIS Peptides About Generic Concept of Site Group. Identification of groups comprising important sites in the macromolecule. They specify residues comprising catalytic, cofactor, anticodon, regulatory sites. Generic Concept describing Binding Site Groups in the Protein Sub Concept containing All Turns and Unknown Folds present in a Protein Sub Concept defining Active Binding Sites present in Protein Sub Concept describing Strand structure starting with one edge of the sheet and continuing to the spatial adjacent strand in a Protein. Sub Concept containing Sequence and 3D Structure description of Protein Structure Residue Details of the Atoms in Protein Structure Atom Details of Protein Structure First Site Group of the Binding Site Chain Details of the Atoms in Protein Structure Reference to concept of Chains Property of the Chain Structural Factor for the Gene Defect Metabolic Factor for the Gene Defect Molecular Dysfunction of the Protein Gene Involved in the defect Genetic Function of Protein Protein Function in an Organism Protein Function in the Cell Property of the Residue Infection causing the Gene Defect Cellular Dysfunction of the Protein Protein Function in an Organ Drug Use causing Gene Defect Protein Function in the Molecule Reference to concept of Residue Complexity of Gene Defect: Single or Multiple Genes Value of electric charge on the atom Sequence Number of End Residue in Strand Reference to concept of Atoms Title for the experiment or analysis that is represented in the Entry. Atom Serial Number Reference to concept of Residues Title of the Citation Modified Residue Details Name and Place of Publication Reference to concept of Residues Residue Name Protein Super Family Describes information about the experiment and identifies the experimental technique used. This may refer to the type of radiation and sample, or include the spectroscopic or modeling technique. Numbers of Strands in the Sheet Identifies the location inside or outside the cell Editors of the Citation Helix Class Larger Biological Unit of which molecule is the part Reference to the concept of Chains Reference to concept of Residues Residue Sequence Number in Previous Strand Site Identifier Contains a set of terms relevant to the entry. Keywords provide a simple means of categorizing entries and may be used to generate index files. It provides the opportunity to add further annotation to the entry in a concise and computer-searchable fashion. Description of the Modification Description of Protein Ontology Protein Family Details of the Structural Domain Additional Information about the Source Sequence Number of Intial Residue Sequence in Turn Reference to concept of Residues Reference to concept of Residues Reference to concept of Chains Reference to concept of Atoms Reference to concept of Chains Reference to concept of Chains Sheet Identifier Name of the Molecule Names of the people responsible for the contents of the entry. Z Value Organized structure within a cell c in angstroms Encoded References to Citation Reference to concept of Residues Number of Residues comprising site System used to express recombinant macromolecules. First Binding Residue Details Specifies a domain or region of the Molecule b in angstroms Identifies the Gene Associated Comment with the Turn Atom Name Molecule involved in Hydrolysis a in angstroms Second Binding Residue Details Describes Mutations in Molecule. One-Alphabet Chain Identifier Identifies Specific Model Z Coordinates of the Atom Original Protein Data Source ID Type of Hydrolysis Identifies the Strain Sequence Number of Binding Residue Defined Expression System Vector Details Reference to concept of Residues Numbers each molecule component Molecule yeilded as a result of Hydrolysis Gene Defect Description Second Binding Atom Details Protein Family Details of the Functional Domain Number of Residues in the Chain Description of any Change due to Hydrolysis Sequence Number of End Residue in the Turn Helix Number Indicates a chemically synthesized source. Sequence Number of Binding Residue Protein Ontology Identifier (like PO000000000n, where n is a integer) Indentifies the Variant Reference to concept of Chains Chain Name Second Binding Atom Details First Binding Atom Details Authors of the Citation Helix Identifier Sequence Number of Intial Residue in the Helix Reference to concept of Atoms Element Symbol for Atom Standard Residue that got modified Orthogonal occupancy of the atom in crystal structure of the molecule. gamma in degrees Reference to concept of Chains Organised Group of Tissues that carries on a specific function Temperature Factor of the Atom Binding Hydrogen Atom Details Turn Identifier Turn Number First Binding Atom Details Recombinant Technology or Chemical Synthesis Scientific Name of the Organism Line of Cells used in the Experiment Strand Number for each strand within the Sheet Sequence Number of Residue to which Atom is attached Sequence Number of the End Residue in the Helix Three-Alphabet Residue Identifier beta in degrees Ogranised Group of Cells with common function and structure Length of the Helix Second Binding Atom Details Source Molecule Identifier alpha in degrees Second Binding Residue Details Common Name of the Organism List of Synonyms for the Molecule Original Protein Data Source Submission Date Protein Family Details of the Entry Reference to concept of Residues Reference to concept of Residues Symmetry Operator Reference to concept of Residues Residue Sequence Number in Current Strand Measure of Angle in degrees Space Group First Binding Residue Details Original Protein Data Source Name Sequence Number of Intial Residue in Strand Identifies specific segments of the molecule X Coordinates of the Atom Identifies a particular cell type Name of Publication or Publication Status Enzyme Commission Number Identifies the secretion Y Coordinates of the Atom Sequence Number of Binding Residue Identifies the Plasmid containing the gene Protein Classification Type Reference to concept of Residues Chain of Modified Residue Protein Family Other Details of the Molecule Reference to concept of Chains Domain or Fragment of the Molecule Symmetry Operator First Binding Atom Details Sense of Strand with respect to the previous strand in the sheet 5-(5-(2,6-DICHLORO-4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)PENTYL)-3-(HYDROXYETHYLOXYMETHYLENEOXYMETHYL) ISOXAZOLE W42 BOC TERT-BUTYLOXYCARBONYL GROUP CPN 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE THF 5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID GLYCEROL GOL NORLEUCINE BORONIC ACID BNO C20 ACETYL-NH-VAL-CYCLOHEXYL-CH2[NCH2CHOH]CH2-BENZYL-VAL-NH-ACETYL CU-O LINKAGE C1O DCI DECARBOXY-ISOLEUCINE PHL L-PHENYLALANINOL U89360E U0E CS CESIUM ION PSEUDOURIDINE PSU (2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYLHEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROANAMIDE IM1 GN7 N7-GUANOSINE-5'-MONOPHOSPHATE 7,8-DIHYDROBIOPTERIN HBI INDENE DEN ALPHA D-GALACTOSE GLA O-SIALIC ACID SIA FAN FORMANILIDE FORMYCIN FMC ORO OROTIC ACID INU N-(3-CYCLOPROPYL(5,6,7,8,9,10-HEXAHYDRO-2-OXO-2H-CYCLOOCTA[B]PYRAN-3-YL)METHYL)PHENYLBENZENSULFONAMIDE 1,2-DIHEXANOYL-3-PENTANOYL PHOSPHOGLYCEROL TC4 F6P FRUCTOSE-6-PHOSPHATE PIPERIDINE PIP MALEIC ACID MAE L-TRYPTOPHANE-PYRIDOXAL-5'-PHOSPHATE SCHIFF BASE PLT 4-O-DEMETHYL-17-DEHYDROXYOXY-DOXORUBICIN DM4 ARA ALPHA-L-ARABINOSE GDB 1-(S-GLUTATHIONYL)-2,4-DINITROBENZENE NICOTINAMIDE 8-BROMO-ADENINE DINUCLEOTIDE PHOSPHATE NBP (N-(2-HYDROXAMATEMETHYLENE-4-METHYL-PENTOYL)PHENYLALANYL)METHYL AMINE HAP AZT 3'-AZIDO-3'-DEOXYTHYMIDINE-5'-TRIPHOSPHATE PHOSPHOTYROSINE PTR 3-HYDROXY-3-CARBOXY-ADIPIC ACID HCA FE (III) ION FE OXY OXYGEN MOLECULE MERCURIBENZOIC ACID MBO BAL BETA-ALANINE (5R,6R)-2,4-BIS-(4-HYDROXY-3-METHOXYBENZYL)-1,5-DIBENZYL-3-OXO-6-HYDROXY-1,2,4-TRIAZACYCLOHEPTANE A88 CU-O-CU LINKAGE C2O 1-METHYL-2-OXY-5,5-DIMETHYL PYRROLIDINE IP4 D-ALANINE DAL ACP 5'-ADENOSYL-METHYLENE-TRIPHOSPHATE TOP TRIMETHOPRIM I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE CLT 4-PHENYL-BUTANOIC ACID LOL LEUCINOL HYDROCINNAMIC ACID HCI 3,4-DIHYDRO-4-OXO-3-((5-TRIFLUOROMETHYL-2-BENZOTHIAZOLYL)METHYL)-1-PHTHALAZINE ACETIC ACID ZST FCB BETA-D-FUCOSE Proline PRO BZF BENZOFURAN HYDROXYAMINO GROUP HOA AUC GOLD (I) CYANIDE ION W71 5-(7-(4-(4,5-DIHYDRO-2-OXAZOLYL)PHENOXY)HEPTYL)-3-METHYL ISOXAZOLE CMC CARBOXYMETHYL COENZYME *A CDR 2,3-DIDEOXYFUCOSE CACODYLATE ION CAC BCT BICARBONATE ION SFG ADENOSYL-ORNITHINE EST ESTRADIOL GUN GUANINE MN2 1-CARBOXYETHYLAMINOMETHYL-4-AMINOMETHYLBENZENE ADENOSINE-2'-MONOPHOSPHATE 2AM 3-SULFINOALANINE CSD H2U 5,6-DIHYDROURIDINE MET Methionine ADENOSINE MONOPHOSPHATE AMP HYP 4-HYDROXYPROLINE OCS CYSTEINESULFONIC ACID U18 (S)-2-(5-(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID TFK 3-[[(METHYLAMINO)SULFONYL]AMINO]-2-OXO-6-PHENYL-N-[3,3,3-TRIFLUORO-1-(1-METHYLETHYL)-2-OXOPHENYL]-1(2H)-PYRIDINE ACETAMIDE DMS DIMETHYL SULFOXIDE GLYCYLMETHYLENE GROUP GCM LYSINE-PYRIDOXAL-5'-PHOSPHATE LLP (METHYLPYRIDAZINE PIPERIDINE BUTYLOXYPHENYL)ETHYLACETATE J80 POE (HYDROXYDIMETHYLENEOXY)OCTANE INDOLE-3-PROPANOL PHOSPHATE IPL PHI IODO-PHENYLALANINE MLY N-DIMETHYL-LYSINE 3-(1-(N-(3-METHYLBUTYL)AMINO-LEUCYL-CARBOXYL)OXIRANE)-2-CARBOXYLIC ACID E6C D-PHENYLALANINE DPN APC 5'-ADENOSYL-PHOSPHATE-METHYLENE-DIPHOSPHATE DIQ DECAHYDRO-1-METHYLISOQUINOLINE-2-CARBONYL U1 URANIUM ATOM 2-((3',5'-DIMETHOXY-4'-HYDROXYPHENYL)AZO)BENZOICACID MOB PNL PROPANAL AAP ALPHA-(2,6-DICHLOROPHENYL)-ALPHA-(2-ACETYL-5-METHYLANILINO)ACETAMIDE MES N-(EHTYLSULFITE)MORPHOLINE MCN PTERIN CYTOSINE DINUCLEOTIDE ACETYL GROUP ACE VX-478 478 ABE ABEQUOSE CYTIDINE-2'-MONOPHOSPHATE C2P GLUCOSE GLC 8-BROMOADENOSINE-5'-DIPHOSPHATE ABP DHB 3,4-DIHYDROXYBENZIC ACID 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE INS COPPER(II) CHLORIDE CUL AUROVERTIN B AUR EG1 AMINOMETHYLENECARBONYLAMINODI(ETHYLOXY)ETHYLAMINOCARBONYLBENZENESULFONAMIDE 4-HYDROXY-3-NITROPHENYLACETYL-EPSILON-AMINOCAPROICACID NP P-HYDROXYBENZALDEHYDE HBA RETINOIC ACID REA TNK 6-BENZYL-1-BENZYLOXYMETHYL-5-ISOPROPYL URACIL HEME-A HEA 2-((3'-METHYL-4'-HYDROXYPHENYL)AZO)BENZOIC ACID MHB 4-(ACETYLAMINO)-3-AMINO BENZOIC ACID