Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Het-PDB Navi.: a database for protein-small molecule interactions.

Akihiro Yamaguchi1, Kei Iida, Nobuaki Matsui

  • 1Department of Bio-Science, Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology, 1266, Tamura-cho, Nagahama, Shiga, 526-0829.

Journal of Biochemistry
|March 5, 2004
PubMed
Summary

Researchers analyzed protein-small molecule interactions in the Protein Data Bank (PDB). They identified common small molecules like metal ions and sugars, and preferred amino acid residues at interaction sites for predicting protein function.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Early steroid initiation may improve outcomes in immune checkpoint inhibitor-related cholangitis: a multicenter cohort study.

Immunological medicine·2026
Same author

A PARK9 iPSC-Derived Dopaminergic Neuron Model Enables Drug Screening Targeting Autophagy-Lysosome Pathway Dysfunction in Parkinson's Disease.

Journal of neurochemistry·2026
Same author

Temporal orchestration of transcriptional and epigenomic programming underlying maternal embryonic diapause in a cricket model.

Communications biology·2026
Same author

Residue interaction chains facilitating the structural change of ND6 subunit in respiratory complex I.

Biochemical and biophysical research communications·2026
Same author

Suppression of ATM kinase signaling accelerates cellular senescence.

Stem cell reports·2026
Same author

Re-examination of the morphological and molecular features of <i>Amanita clarisquamosa</i> and <i>Amanita avellaneosquamosa</i> based on specimens collected in Hokkaido.

Mycoscience·2026

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Genomic sequencing provides protein information, but biological functions require understanding protein interactions.
  • Protein function is determined by interactions with other molecules, including small molecules.
  • Predicting protein function from genomic data necessitates knowledge of protein-small molecule interactions.

Purpose of the Study:

  • To compile and analyze known protein-small molecule interactions from the Protein Data Bank (PDB).
  • To identify common small molecules interacting with proteins and preferred amino acid residues at these interaction sites.
  • To establish a basis for predicting protein function using genomic sequence and 3D structure data.

Main Methods:

  • Surveyed 20,685 entries in the Protein Data Bank (PDB) as of April 2003.

Related Experiment Videos

  • Identified and categorized 4,189 types of small molecules interacting with proteins.
  • Analyzed amino acid residue preferences at protein-small molecule interaction sites.

    • Main Results:

    • Identified metal ions (calcium, zinc, magnesium), sugars, and nucleotides as the most common interacting small molecules.
    • These small molecules often function as enzyme cofactors or protein stabilizers.
    • Discovered specific amino acid residue preferences at interaction sites for each protein-small molecule pair.

    Conclusions:

    • The identified preferences in amino acid residues at interaction sites can serve as a foundation for predicting protein function.
    • The Het-PDB Navi database compiles this interaction data, aiding future research.
    • This work facilitates functional annotation of proteins based on structural and sequence information.