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Related Concept Videos

Valence Bond Theory02:42

Valence Bond Theory

Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
Valence Bond Theory02:45

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Overview of Valence Bond Theory
Crystal Field Theory - Octahedral Complexes02:58

Crystal Field Theory - Octahedral Complexes

Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
CFT focuses on...
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
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Ligand Binding Sites02:40

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Ligand Binding Sites02:40

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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Updated: Jun 8, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Ligands in PSI structures.

Abhinav Kumar1, Hsiu Ju Chiu, Herbert L Axelrod

  • 1Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.

Acta Crystallographica. Section F, Structural Biology and Crystallization Communications
|October 15, 2010
PubMed
Summary
This summary is machine-generated.

Approximately 65% of Protein Structure Initiative (PSI) structures contain bound ligands. Analyzing these ligands provides functional insights for uncharacterized proteins and aids in structural annotation.

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Area of Science:

  • Structural biology
  • Biochemistry
  • Bioinformatics

Background:

  • The Protein Structure Initiative (PSI) has generated a large repository of protein structures.
  • Many PSI structures contain bound ligands, which can influence protein function and stability.
  • Understanding the role of these ligands is crucial for protein annotation and functional characterization.

Purpose of the Study:

  • To describe the methods used at the Joint Center for Structural Genomics (JCSG) for handling and analyzing bound ligands in PSI structures.
  • To survey and analyze the types, variety, and frequency of ligands observed in PSI structures.
  • To illustrate how bound ligands provide functional clues for annotating proteins with limited prior characterization.
  • To introduce a web server developed for mining PSI structures for bound ligands and other features.

Main Methods:

  • Analysis of ligand content in PSI crystal structures.
  • Compilation and statistical analysis of ligand types, variety, and frequency.
  • Development of a web server for ligand and feature analysis.
  • Case studies illustrating ligand-assisted protein functional annotation.

Main Results:

  • Approximately 65% of PSI structures contain bound ligands.
  • A diverse range of ligand types were identified and analyzed.
  • Bound ligands were shown to provide significant functional insights for previously uncharacterized proteins.
  • A functional web server was developed and made available for researchers.

Conclusions:

  • Bound ligands are prevalent in PSI structures and offer valuable functional information.
  • Systematic analysis of ligands enhances protein annotation and understanding.
  • The developed web server serves as a valuable tool for structural biology research.