4TY0

Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase in complex with linear intermediate 5' pppA(3',5')pG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.173

Literature

Macromolecules
Sequence Display for 4TY0

Classification: TRANSFERASE

Total Structure Weight: 95907.80

Macromolecule Entities
Molecule Chains Length Organism Details
Cyclic AMP-GMP synthase A, B 413 Vibrio cholerae Gene Name(s): dncV VC_0179
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
38V
Query on 38V

A, B [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,4R,5R)- 5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)- 3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl- phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methoxy- [[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic acid
C21 H30 N10 O19 P4
QFHKDAVOJDVDDK-XPWFQUROSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.173
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 70.33 α = 90.00
b = 59.60 β = 96.47
c = 102.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-07-07
  • Released Date: 2014-08-13
  • Deposition author(s): Kranzusch, P.J., Lee, A.S.Y., Wilson, S.C., Solovykh, M.S., Vance, R.E., Berger, J.M., Doudna, J.A.

Revision History

  • 2014-09-03
    Type: Database references
  • 2014-10-01
    Type: Database references
  • 2015-02-04
    Type: Derived calculations