PSPH Human phosphoserine phosphatase

Experimental Data Snapshot

  • Resolution: 1.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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This is version 2.2 of the entry. See complete history


Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase.

Haufroid, M.Mirgaux, M.Leherte, L.Wouters, J.

(2019) Acta Crystallogr D Struct Biol 75: 592-604

  • DOI: https://doi.org/10.1107/S2059798319006867
  • Primary Citation of Related Structures:  
    6HYJ, 6HYY, 6Q6J

  • PubMed Abstract: 

    The equilibrium between phosphorylation and dephosphorylation is one of the most important processes that takes place in living cells. Human phosphoserine phosphatase (hPSP) is a key enzyme in the production of serine by the dephosphorylation of phospho-L-serine. It is directly involved in the biosynthesis of other important metabolites such as glycine and D-serine (a neuromodulator). hPSP is involved in the survival mechanism of cancer cells and has recently been found to be an essential biomarker. Here, three new high-resolution crystal structures of hPSP (1.5-2.0 Å) in complexes with phosphoserine and with serine, which are the substrate and the product of the reaction, respectively, and in complex with a noncleavable substrate analogue (homocysteic acid) are presented. New types of interactions take place between the enzyme and its ligands. Moreover, the loop involved in the open/closed state of the enzyme is fully refined in a totally unfolded conformation. This loop is further studied through molecular-dynamics simulations. Finally, all of these analyses allow a more complete reaction mechanism for this enzyme to be proposed which is consistent with previous publications on the subject.

  • Organizational Affiliation

    Namur Medicine and Drug Innovation Center, Namur Research Institute for Life Science (NAMEDIC-NARILIS), Department of Chemistry, Laboratoire de Chimie Biologique Structurale (CBS), University of Namur (UNamur), 61 Rue de Bruxelles, 5000 Namur, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoserine phosphatase
A, B
224Homo sapiensMutation(s): 0 
Gene Names: PSPH
UniProt & NIH Common Fund Data Resources
Find proteins for P78330 (Homo sapiens)
Explore P78330 
Go to UniProtKB:  P78330
PHAROS:  P78330
GTEx:  ENSG00000146733 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78330
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.93 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.67α = 90
b = 128.97β = 90
c = 155.71γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references
  • Version 2.0: 2019-10-02
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2022-12-07
    Changes: Advisory, Database references, Derived calculations
  • Version 2.2: 2024-01-31
    Changes: Data collection, Refinement description