3EGH

Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R

Structural Biology Knowledgebase: 3EGH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.192

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EGH

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 114119.72

Macromolecule Entities
Molecule Chains Length Organism Details
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit A, B 329 Homo sapiens EC#: 3.1.3.16 IUBMB
Gene Name(s): PPP1CA Gene View PPP1A
Spinophilin C, D 170 Rattus norvegicus Fragment: PP1 binding and PDZ domains
Gene Name(s): Ppp1r9b
nodularin R E, F 5 Nodularia spumigena

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
GOL
Query on GOL

A, C GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000214 (ACB,FGA,ARG,MDH,1ZN) E NODULARIN-R Oligopeptide /
Toxin
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.192
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 119.41 α = 90.00
b = 84.43 β = 93.58
c = 109.31 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-10
  • Released Date: 2010-03-23
  • Deposition author(s): Ragusa, M.J., Page, R., Peti, W.

Revision History

  • 2013-04-10
    Type: Biological assembly | Details: --
  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence