Skip to main content
Fig. 6 | Biology Direct

Fig. 6

From: Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site

Fig. 6

Positional fluctuation (RMSF) of the GPAA1 models with/without binding to PEP. The diagram in the lower part of the figure shows that four large loops have particularly extensive motions during molecular dynamics simulations regardless of the substrate and one/duo zinc ion binding modes. These loops are labelled as (1) residues 111–130, (2) residues 197–215, (3) residues 240–250, and (4) residues 276–299 including a small helix (훼x as predicted in reference [23]). An illustration of the 4 loop motions (in the case of the GPAA1Zn model) are shown on the top of the figure with grey arrows indicating the motion vectors, the length of which represents the magnitude of the movements. The GPAA1 structure is shown with helices in cyan, strands in red, and loops in magenta. The five Zn-binding residues are represented by their Cα atoms as coloured spheres. The zinc ion is presented as a grey sphere

Back to article page