PDBCharges

PDBCharges is a web application providing partial atomic charges of protein structures from the Protein Data Bank. The charges are computed by the semiempirical quantum mechanical methods GFN1-xTB and reproduce the PBE0/TZVP/CM5 charges. Before computation of the charges, hydrogens are added to the structure by Hydride and MoleculeKit at pH 7.2. The positions of the added hydrogens are also optimized using the GFN-FF force-field. The details about the methodology and usage are described in the manual. This website is free and open to all users and there is no login requirement. Source codes are freely available at GitHub.

Examples

Phospholipase inhibited by ibuprofen
P-glycoprotein
Phospholipase A2 is an enzyme that occurs in plants, mammals, snakes, and bee venoms. It catalyses the hydrolysis of the ester bond in phospholipids in the cell membranes. Hydrolysis products are lysophosphatidic acid and free fatty acids, which can disrupt cellular membranes and induce inflammatory responses (Burke2010). The carboxyl group of ibuprofen interact, creating an electrostatic bond to lysin (LYS 69) in phospholipase A2 and inhibiting its function. Based on this knowledge, we can develop therapeutics that can reduce the inflammatory reactions associated with snakebites (Gaspar2010).
Carbohydrate binding lectin
P-glycoprotein
Lectin PA-IIL from the bacteria Pseudomonas aeruginosa plays a key role in its pathogenicity (i.e., it can cause cystic fibrosis, which has high mortality) (Imberty2004). This lectin has an unusually high affinity for carbohydrates due to its unique binding mode involving two calcium ions (Mitchell2002). The calcium ions form ionic bonds with aspartic acid residues (chain A: ASP 96, ASP 99, ASP 101 and ASP 104) in the protein and with three hydroxyl groups of the fucose molecule (chain A: FUC 999). This interaction results in a stable complex through extensive charge delocalisation. Unlike most protein-carbohydrate interactions, PA-IIL relies on ionic and coordination bonds with minimal hydrophobic bonds, presenting the structural role of calcium ions in stabilising the binding site (Mitchell2005).
Potassium channel
P-glycoprotein
TASK2 (TWIK-related acid-sensitive K+ channel 2) is a pH-gated ion channel belonging to the two-pore domain K+ (K2P) channel family (Reyes1998). This channel maintains cellular homeostasis and regulates physiological responses to environmental changes. The transmembrane regions of TASK2 are characterised by their nonpolar nature and lack of charge, distinguishing them from the intracellular and extracellular domains of the protein (Li2020).
Are you interested in a research collaboration? Feel free to contact us.
ELIXIR logo
PDBCharges tool is a part of services provided by ELIXIR – European research infrastructure for biological information.
For other services provided by ELIXIR's Czech Republic Node visit www.elixir-czech.cz/services.
Licence conditions in accordance with § 11 of Act No. 130/2002 Coll. The owner of the software is Masaryk University, a public university, ID: 00216224. Masaryk University allows other companies and individuals to use this software free of charge and without territorial restrictions in usual way, that does not depreciate its value. This permission is granted for the duration of property rights. This software is not subject to special information treatment according to Act No. 412/2005 Coll., as amended. In case that a person who will use the software under this licence offer violates the licence terms, the permission to use the software terminates.