5DPF

Thermolysin in complex with inhibitor.

Summary for 5DPF

• Entry DOI: 10.2210/pdb5dpf/pdb
• Related: 5DPE
• Descriptor: Thermolysin, N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-4-methyl-L-leucine, ZINC ION, ... (7 entities in total)
• Functional Keywords: protease, metalloprotease, hydrolase, hydrolase inhibitor complex
• Biological source: Bacillus thermoproteolyticus
• Cellular location: Secreted: P00800
• Total number of polymer chains: 1
• Total formula weight: 35660.38

Authors

Krimmer, S.G.,Heine, A.,Klebe, G. (deposition date: 2015-09-12, release date: 2015-10-28, Last modification date: 2024-01-10)

Primary citation

Krimmer, S.G.,Klebe, G.
Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.
J. Comput. Aided Mol. Des., 29:867-883, 2015

PubMed Abstract: For a conscientious interpretation of thermodynamic parameters (Gibbs free energy, enthalpy and entropy) obtained by isothermal titration calorimetry (ITC), it is necessary to first evaluate the experimental setup and conditions at which the data were measured. The data quality must be assessed and the precision and accuracy of the measured parameters must be estimated. This information provides the basis at which level discussion of the data is appropriate, and allows insight into the significance of comparisons with other data. The aim of this article is to provide the reader with basic understanding of the ITC technique and the experimental practices commonly applied, in order to foster an appreciation for how much measured thermodynamic parameters can deviate from ideal, error-free values. Particular attention is paid to the shape of the recorded isotherm (c-value), the influence of the applied buffer used for the reaction (protonation reactions, pH), the chosen experimental settings (temperature), impurities of protein and ligand, sources of systematic errors (solution concentration, solution activity, and device calibration) and to the applied analysis software. Furthermore, we comment on enthalpy-entropy compensation, heat capacities and van't Hoff enthalpies.

PubMed: 26376645
DOI: 10.1007/s10822-015-9867-y

Experimental method

X-RAY DIFFRACTION (1.47 Å)