3MK0: Refinement of Placental Alkaline Phosphatase Complexed With Nitrophenyl

Citation:
Abstract
In order to gain deeper insights into the functional sites of human placental alkaline phosphatase, the structures of the enzyme with the putative regulators L-Phe, pNPP and 5'-AMP [Llinas et al. (2005), J. Mol. Biol. 350, 441-451] were re-refined. Significant variations in ligand positioning and identity were found compared with the previous report. The multiple corrections to the model improved the phases and the electron-density maps, allowing the modeling of omitted side chains and multiple disordered residues. These improvements led to a change in the position of L-Phe at the peripheral binding site, which appeared to be reversed. The structure with pNPP contained only p-nitrophenol in three distinct sites, while the structure with 5'-AMP contained the p-nitrophenyl group in two of the sites instead of 5'-AMP. Comparison of the re-refined models shows a consistent pattern of interactions at the peripheral site.
PDB ID: 3MK0Download
MMDB ID: 88040
PDB Deposition Date: 2010/4/13
Updated in MMDB: 2011/10 
Experimental Method:
x-ray diffraction
Resolution: 1.9  Å
Source Organism:
Similar Structures:
Biological Unit for 3MK0: dimeric; determined by author and by software (PISA)
Molecular Components in 3MK0
Label Count Molecule
Proteins (2 molecules)
2
Alkaline Phosphatase, Placental Type
Molecule annotation
Chemicals (20 molecules)
1
4
2
4
3
2
4
2
5
4
6
2
7
2
* Click molecule labels to explore molecular sequence information.

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