3E7A | pdb_00003e7a

Crystal Structure of Protein Phosphatase-1 Bound to the natural toxin Nodularin-R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.169 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.143 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 
    0.144 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

Crystal structures of protein phosphatase-1 bound to nodularin-R and tautomycin: a novel scaffold for structure-based drug design of serine/threonine phosphatase inhibitors

Kelker, M.S.Page, R.Peti, W.

(2009) J Mol Biology 385: 11-21

  • DOI: https://doi.org/10.1016/j.jmb.2008.10.053
  • Primary Citation Related Structures: 
    3E7A, 3E7B

  • PubMed Abstract: 

    Protein phosphatase 1 occurs in all tissues and regulates many pathways, ranging from cell-cycle progression to carbohydrate metabolism. Many naturally occurring, molecular toxins modulate PP1 activity, though the exact mechanism of this differential regulation is not understood. A detailed elucidation of these interactions is crucial for understanding the cellular basis of phosphatase function and signaling pathways but, more importantly, they can serve as the basis for highly specific therapeutics, e.g. against cancer. We report the crystal structures of PP1 in complex with nodularin-R at 1.63 A and tautomycin at 1.70 A resolution. The PP1:nodularin-R complex was used to demonstrate the utility of our improved PP1 production technique, which produces highly active, soluble PP1. Tautomycin is one of the few toxins that reportedly preferentially binds PP1>PP2A. Therefore, the PP1:tautomycin structure is the first complex structure with a toxin with preferred PP1 specificity. Furthermore, since tautomycin is a linear non-peptide-based toxin, our reported structure will aid the design of lead compounds for novel PP1-specific pharmaceuticals.


  • Organizational Affiliation
    • Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI 02903, USA.

Macromolecule Content 

  • Total Structure Weight: 72.42 kDa 
  • Atom Count: 5,652 
  • Modeled Residue Count: 596 
  • Deposited Residue Count: 608 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
A, B
299Homo sapiensMutation(s): 0 
Gene Names: PPP1CAPPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
PHAROS:  P62136
GTEx:  ENSG00000172531 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62136
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
nodularin R
C, D
5Nodularia spumigenaMutation(s): 0 

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD

Query on IOD



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
DA [auth B],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
R [auth B],
S [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
AZI

Query on AZI



Download:Ideal Coordinates CCD File
BA [auth B],
CA [auth B]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth B],
N [auth A],
O [auth A],
P [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.169 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.143 (Depositor), 0.152 (DCC) 
  • R-Value Observed: 0.144 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.354α = 90
b = 77.274β = 90
c = 132.444γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-02-27
    Changes: Other
  • Version 1.3: 2013-04-10
    Changes: Derived calculations
  • Version 1.4: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations