1ZED

Alkaline phosphatase from human placenta in complex with p-nitrophenyl-phosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 3MK1


Literature

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: 441-451

  • DOI: https://doi.org/10.1016/j.jmb.2005.04.068
  • Primary Citation of Related Structures:  
    1ZEB, 1ZED, 1ZEF

  • PubMed Abstract: 

    The activity of human placental alkaline phosphatase (PLAP) is downregulated by a number of effectors such as l-phenylalanine, an uncompetitive inhibitor, 5'-AMP, an antagonist of the effects of PLAP on fibroblast proliferation and by p-nitrophenyl-phosphonate (PNPPate), a non-hydrolysable substrate analogue. For the first two, such regulation may be linked to its biological function that requires a reduced and better-regulated hydrolytic rate. To understand how such disparate ligands are able to inhibit the enzyme, we solved the structure of the complexes at 1.6A, 1.9A and 1.9A resolution, respectively. These crystal structures are the first of an alkaline phosphatase in complex with organic inhibitors. Of the three inhibitors, only l-Phe and PNPPate bind at the active site hydrophobic pocket, providing structural data on the uncompetitive inhibition process. In contrast, all three ligands interact at a remote peripheral site located 28A from the active site. In order to extend these observations to the other members of the human alkaline phosphatase family, we have modelled the structures of the other human isozymes and compared them to PLAP. This comparison highlights the crucial role played by position 429 at the active site in the modulation of the catalytic process, and suggests that the peripheral binding site may be involved in the functional specialization of the PLAP isozyme.


  • Organizational Affiliation

    Laboratoire de Structure des Protéines, Département d'Ingénierie et d'Etude des Protéines, Commissariat à l'Energie Atomique, 91191 Gif sur Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alkaline phosphatase484Homo sapiensMutation(s): 0 
EC: 3.1.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05187 (Homo sapiens)
Go to UniProtKB:  P05187
PHAROS:  P05187
GTEx:  ENSG00000163283 
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P05187-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PNP
Query on PNP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
METHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER
C7 H8 N O5 P
VJPXTXIEAOSJBR-UHFFFAOYSA-N
PO3
Query on PO3

Download Ideal Coordinates CCD File 
H [auth A]PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.346α = 90
b = 114.573β = 90
c = 106.568γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary