3DC5

Crystal Structure of a manganese superoxide dismutases from Caenorhabditis elegans

Structural Biology Knowledgebase: 3DC5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DC5

Classification: OXIDOREDUCTASE

Total Structure Weight: 44931.26

Macromolecule Entities
Molecule Chains Length Organism Details
Superoxide dismutase [Mn] 2 A, C 195 Caenorhabditis elegans EC#: 1.15.1.1 IUBMB
Gene Name(s): sod-3 C08A9.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, C MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.189
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.78 α = 90.00
b = 81.78 β = 90.00
c = 136.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-03
  • Released Date: 2009-06-09
  • Deposition author(s): Trinh, C.H., Hunter, T., Stewart, E.E., Phillips, S.E.V., Hunter, G.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor