3F9Q
Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.
Summary for 3F9Q
| Entry DOI | 10.2210/pdb3f9q/pdb |
| Related | 1LF4 |
| Descriptor | Plasmepsin-2 (2 entities in total) |
| Functional Keywords | hydrolase, aspartyl protease, glycoprotein, protease, vacuole, zymogen |
| Biological source | Plasmodium falciparum |
| Cellular location | Vacuole: P46925 |
| Total number of polymer chains | 1 |
| Total formula weight | 36909.62 |
| Authors | Robbins, A.H.,Mckenna, R. (deposition date: 2008-11-14, release date: 2009-03-10, Last modification date: 2024-10-16) |
| Primary citation | Robbins, A.H.,Dunn, B.M.,Agbandje-McKenna, M.,McKenna, R. Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank. Acta Crystallogr.,Sect.D, 65:294-296, 2009 Cited by PubMed Abstract: The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position. PubMed: 19237752DOI: 10.1107/S0907444908041632 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.9 Å) |
Structure validation
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