2RDE

Crystal structure of VCA0042 complexed with c-di-GMP

Structural Biology Knowledgebase: 2RDE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 2RDE

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 57874.15

Macromolecule Entities
Molecule Chains Length Organism Details
Uncharacterized protein VCA0042 A, B 251 Vibrio cholerae Gene Name(s): VC0395_0091 VC395_A0038
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C2E
Query on C2E

A, B 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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C2E N/A in BindingDB
Kd: 97.1 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.209
  • R-Value Work: 0.195
  • Space Group: P 1

Unit Cell:

Length (Å) Angle (°)
a = 47.01 α = 99.88
b = 55.40 β = 97.09
c = 58.04 γ = 106.80

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-09-22
  • Released Date: 2007-10-30
  • Deposition author(s): Benach, J., Swaminathan, S.S., Tamayo, R., Seetharaman, J., Handelman, S., Forouhar, F., Neely, H., Camilli, A., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4