3QPE

Crystal structure of Galacturonate Dehydratase from GEOBACILLUS SP. complexed with D-Galacturonate and 5-keto-4-deoxy-D-Galacturonate

Structural Biology Knowledgebase: 3QPE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QPE

Classification: METAL BINDING PROTEIN

Total Structure Weight: 176703.85

Macromolecule Entities
Molecule Chains Length Organism Details
Mandelate racemase/muconate lactonizing protein A, B, C, D 392 Paenibacillus sp. y412mc10 Gene Name(s): GYMC10_3367

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGU
Query on DGU

A D-galacturonic acid
D-Galacturonate (Synonym)
C6 H10 O7
IAJILQKETJEXLJ-RSJOWCBRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D54
Query on D54

B, C, D 4-deoxy-L-threo-hex-5-ulosuronic acid
5-keto-4-deoxy-D-Galacturonate (Synonym)
C6 H8 O6
IMUGYKFHMJLTOU-UCORVYFPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.221
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 158.02 α = 90.00
b = 66.26 β = 95.73
c = 154.61 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-02-12
  • Released Date: 2012-02-15
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F., Gerlt, J.A., Almo, S.C.

Revision History

No revisions since initial release