4HJF

EAL domain of phosphodiesterase PdeA in complex with c-di-GMP and Ca++


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.168

Literature

Macromolecules
Sequence Display for 4HJF

Classification: SIGNALING PROTEIN

Total Structure Weight: 37551.32

Macromolecule Entities
Molecule Chains Length Organism Details
GGDEF family protein A 340 Caulobacter vibrioides Gene Name(s): CC_3396
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C2E
Query on C2E

A 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)- 3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro- 2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine- 2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin- 6-one)
c-di-GMP, Cyclic diguanosine monophosphate (Synonym)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 62.20 α = 90.00
b = 63.19 β = 90.00
c = 66.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-10-12
  • Released Date: 2012-10-31
  • Deposition author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Massa, C., Schirmer, T., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2012-10-31

    Type: Initial release

  • Version 1_1: 2016-08-31

    Type: Structure summary

  • Version 1_2: 2016-10-12

    Type: Structure summary

  • Version 1_3: 2017-11-15

    Type: Refinement description