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STRENDADB_light_20240722.md

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STRENDA DB

Administration

Data

Publication

This is the publication that includes the experimental results of an enzyme kinetics characterization.

  • Title
    • type: string
    • description: title of the publication
  • DOI
    • type: string
    • description: identifier of the publication
  • PMID
    • type: string
    • description: identifier of the publication as indexed in PubMed
  • Author
    • type: Author
    • Multiple: true
  • Experiment
    • type: Experiment
    • Multiple: true

Author

  • Name
    • type: string
    • description: name of the author. Nomenclature: Family name initials first name
  • Affiliation
    • type: string
    • description: name of organizaton, department, city, country
  • Email
    • type: string
    • description: email address
  • ORCID
    • type: string
    • description: ORCID idenfier

Experiment

  • Name of Experiment
    • type: string
    • description: name of the experiment, just for internal purposes
  • Type of Assay
    • type: string
    • description: name of the assay
  • Direction of the Assay
    • type: string
    • description:
  • Definition of the compound monitored
    • type: string
    • description:
  • Continuously monitored
    • type: string
    • description: selection of the stopping procedure
    • type: string
    • description: other
    • type: string
  • Directly monitored
    • type: string
  • Protein Assay
    • type: ProteinDescription
    • Multiple: false

ProteinDescription

  • UniProtKB AC
    • type: string
    • description: identifier obtained from UniProtKB
  • Protein name
    • type: string
    • description: name of the protein as of UniProtKB
  • Protein Sequence
    • type: SequenceModifications
    • description: amino acid sequence as from UniProtKB
  • Modifications
    • type: Modifications
  • Protein Source
    • type: ProteinSource
  • Reaction
    • type: ProteinReaction
  • Protein characterization
    • type: Dataset
    • Multiple: true

ProteinSource

  • Expression system
    • type: string
    • description: description of expression system if heterologously expressed
  • Organism
    • type: string
    • description: as in UniProtKB provided, name of organism
  • Taxon ID
    • type: string
    • description: ID as obtained from NCBI Taxonomy
  • Strain
    • type: string
    • description: name or identifier of the strain
  • Cell Type
    • type: string
    • description: determination of the cell in which the protein is expressed
  • Tissue
    • type: string
    • description: determination of the tissue, ideally BTO is used
  • Localization
    • type: string
    • description: determination of the localization (membran, cytosol, etc.)

SequenceModifications

  • Sequence modification
    • type: string
    • description: modified amino acid sequence
  • Specification of the type of modification
    • type: string
    • description: description of the types of modifications
  • Determination of PTM
    • type: string
    • description: Phosphorylation, Glycosylation, Acetylation, Hydroxylation, Methylation, Other

ProteinReaction

  • EC number
    • type: string
    • description: EC number obtained from ExplorEnz
  • Reaction as in ExplorEnz
    • type: string
    • description: reaction as described in ExplorEnz
  • Comment
    • type: string
    • description: comment on the protein reaction if not properly described in ExplorEnz

Dataset

  • Name
    • type: string
    • description: name of the dataset
  • Assay conditions
    • type: AssayConditions
    • Multiple: true
  • Results Set
    • type: ResultsSet
    • Multiple: true
  • DOI
    • type: string
    • description: DOI of the dataset

AssayConditions

  • Small Assay Components
    • type: Small_Assay_Components
    • description: description of the compound used in the assay
  • Macromolecular Components
    • type: Macromolecular_Components
    • description: description of the macromolecular components
  • Concentration of the assayed protein
    • type: string
    • description: value with unit
  • Description of concentration measurement
    • type: string
    • description: free text field
  • pH
    • type: string
    • description: value and unit
  • pD
    • type: string
    • description: value and unit
  • Temperature
    • type: string
    • description: value and unit, K and Celsius

Small_Assay_Components

  • Role
    • type: Role_of_Component
    • description: role in the assay, i.e. substrate, product, etc.
  • Initial concentration - fixed
    • type: string
    • description: unit, value
  • Initial concentration - varied
    • type: string
    • description: concentration range, value, unit
  • Compound name
    • type: string
    • description: name as obtained from PubChem
  • InChi
    • type: string
    • description: InChi string
  • IUPAC
    • type: string
    • description: IUPAC name
  • ChEBI ID
    • type: string
    • description: identifier
  • PubChem CID
    • type: string
    • description: identifier

Macromolecular_Components

  • Role
    • type: Role_of_Component
    • description: role in the assay, i.e. substrate, product, etc.
  • Initial concentration - fixed
    • type: string
    • description: unit, value
  • Initial concentration - varied
    • type: string
    • description: concentration range, value, unit
  • Class
    • type: Class
    • description: protein, carbohydrate, DNA, RNA, etc.
  • Compound name
    • type: string
    • description: name as obtained from PubChem
  • InChi
    • type: string
    • description: InChi string
  • IUPAC
    • type: string
    • description: IUPAC name
  • Database used
    • type: string
    • description: name of the database
  • Identifier
    • type: string
    • description: identifier

Role_of_Component

  • Substrate
    • type: string
    • description: substrate of chemical reaction
  • Product
    • type: string
    • description: production of chemical reaction
  • Inhibitor
    • type: string
    • description: component that inhibits the chemical reaction
  • Activator
    • type: string
    • description: component that activates/enhances the chemical reaction

Class

  • Protein
    • type: string
  • Carbohydrate
    • type: string
  • DNA
    • type: string
  • RNA
    • type: string
  • Lipid
    • type: string
  • Other
    • type: string

ResultsSet

  • Initial Kinetic Parameters
    • type: Initial_Kinetics_Parameters
    • description: Km, kcat, V, kcat/Km, V/Km
  • Activation
    • type: Activation
  • Inhibition
    • type: Inhibition

Initial_Kinetics_Parameters

  • Km
    • type: string
    • descriptor: value, SE, unit
  • kcat
    • type: string
    • descriptor: value, SE, unit
  • V
    • type: string
    • descriptor: value, SE, unit
  • kcat/Km
    • type: string
    • descriptor: value, SE, unit
  • V/Km
    • type: string
    • descriptor: value, SE, unit

Activation

  • Affinity constant
    • type: string
    • descriptor: value, SE, unit, true or apparent
  • Reaction velocity
  • no activator
    • type: string
    • description: velocity without activator
  • at max. concentration
    • type: string
    • description: velocity at maximum concentration of activator
  • Saturation
    • type: string
    • description: statement whether the concentration was saturating or not
  • Influence on substrate MM kinetics
    • Km no activator
      • type: string
      • description: Value, SE, Unit, true/apparent
    • at max. concentration
      • type: string
      • description: Value, SE, Unit, true/apparent

Inhibition

  • Reversibility_yes
    • type: string
    • description: competitive, uncompetitive, mixed, kic, SE, Unit, Math function
  • Reversibility_no
    • type: string
    • description: ki, SE, Unit, Comment