2BDX

X-ray Crystal Structure of dihydromicrocystin-LA bound to Protein Phosphatase-1

Structural Biology Knowledgebase: 2BDX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.212

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BDX

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 38071.04

Macromolecule Entities
Molecule Chains Length Organism Details
Serine/threonine protein phosphatase PP1-gamma catalytic subunit A 323 Homo sapiens EC#: 3.1.3.16 IUBMB
Gene Name(s): PPP1CC Gene View
DIHYDROMICROCYSTIN-LA B 7 Microcystis aeruginosa Mutation: X7X

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MN
Query on MN

A 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_000215 (ACB,ALA,FGA,DAL,LEU,1ZN,MAA) B DIHYDROMICROCYSTIN-LA Oligopeptide /
Toxin
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) 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: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.212
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 99.98 α = 90.00
b = 99.98 β = 90.00
c = 62.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-21
  • Released Date: 2006-01-17
  • Deposition author(s): Maynes, J.T., Luu, H.A., Cherney, M.M., Andersen, R.J., Williams, D., Holmes, C.F., James, M.N.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-27
    Type: Version format compliance | Details: added version revdat
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 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: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence