The carboxyl group of the Kcx residue is commonly found in contact with positively charged ion(s). In 41 of the 62 protein structures, carboxylated lysine residues interact with metal ions in either single or multiple metal-ion centers.

Jan 5, 2023 · I began my journey with drawing the KCX residue with a charge -1 and ACE and NME caps on each side of the residue there the protien continues. I performed a MMFF94 geometry optimization to get a 3D structure, saved it as -mol2 file and used OpenBabel to convert it …

KCX-150 is lysine-like residue, right? Simply, optimize the geometry first, then calculate the partial charges and create a topology file. Your approach is reasonable. Moreover, In this case,...

the Kcx residue, we did not include the carboxyl group of the Kcx residue. Instead, we projected an atom (named pCX for projected CarboXyl group) onto the tip of the NZ atom of both the Kcx and the Lys side chains, taking as a direction the average direction of the remaining atoms of …

Oct 21, 2024 · During this process, I encountered an issue with a non-standard residue in the protein's main chain. I had previously sought advice and was advised to customize the KCX residue and then provide the frcmod and mol2 parameters to …

Oct 26, 2024 · The short answer is “customize this KCX residue and then feed the frcmod plus mol2 parameters to both MCPB.py’s and tleap’s input files”.

Yellow dots represent amino acids that are part of the KCX site and the red dot represents the Kcx residue (only 1ejx, 3kdn and 3isg shown). The left axis shows the PDB code (PDB ID) and the right axis the percentage of the extent of the protein sequences that the KCX sites occupy.

Jan 3, 2019 · In some cases, the modified lysine is directly involved in the enzymatic reactions; for example, in class D β-lactamase the nonmetal-coordinated carboxylated lysine residue (KCX) functions as a general base during the catalysis , and in RuBisCO a lysyl carbamate is required for the substrate decarboxylation to initiate the reaction .

ABSTRACT: Antibiotic-resistant Enterobacterales that produce oxacillinase (OXA)-48-like Class D β-lactamases are often linked to increased clinical mortality. Though the catalytic mechanism of OXA-48 is known, the molecular origin of its biphasic kinetics has been elusive.

A fragment of 40 amino acids was extracted with the Kcx residue in the center of each protein sequence. The resulting multiple sequence alignment was used to create a sequence logo (Crooks