6PWK

Vibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Vibrio cholerae LapD S helix-GGDEF-EAL (bound to c-di-GMP)

Giglio, K.M.Cooley, R.B.Sondermann, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GGDEF and EAL domain-containing protein
A, B
418Vibrio choleraeMutation(s): 0 
Gene Names: yhjK
Find proteins for A0A0H6T0A6 (Vibrio cholerae)
Go to UniProtKB:  A0A0H6T0A6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download SDF File 
Download CCD File 
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
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.379α = 90.00
b = 90.221β = 115.49
c = 82.750γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM123609
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103485
National Science Foundation (United States)United StatesDMR-1332208

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release