3MK0

Refinement of placental alkaline phosphatase complexed with nitrophenyl


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:1zeb


Literature

Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site.

Stec, B.Cheltsov, A.Millan, J.L.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 866-870

  • DOI: 10.1107/S1744309110019767
  • Primary Citation of Related Structures:  
    3MK0, 3MK1, 3MK2

  • PubMed 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 ...

    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.


    Related Citations: 
    • Structural studies of human placental alkaline phosphatase in complex with functional ligands.
      Llinas, P., Stura, E.A., Menez, A., Kiss, Z., Stigbrand, T., Millan, J.L., Le Du, M.H.
      (2005) J Mol Biol 350: 441

    Organizational Affiliation

    Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA. bstec@burnham.org



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alkaline phosphatase, placental type A484Homo sapiensMutation(s): 0 
Gene Names: ALPPPLAP
EC: 3.1.3.1
Find proteins for P05187 (Homo sapiens)
Explore P05187 
Go to UniProtKB:  P05187
NIH Common Fund Data Resources
PHAROS:  P05187
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.137 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.022α = 90
b = 113.894β = 90
c = 106.594γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary