6DGM

Streptococcus pyogenes phosphoglycerol transferase GacH in complex with sn-glycerol-1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of glycerol phosphate modification on streptococcal rhamnose polysaccharides.

Edgar, R.J.van Hensbergen, V.P.Ruda, A.Turner, A.G.Deng, P.Le Breton, Y.El-Sayed, N.M.Belew, A.T.McIver, K.S.McEwan, A.G.Morris, A.J.Lambeau, G.Walker, M.J.Rush, J.S.Korotkov, K.V.Widmalm, G.van Sorge, N.M.Korotkova, N.

(2019) Nat. Chem. Biol. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphoglycerol transferase GacH
A, B
383Streptococcus pyogenes serotype M28 (strain MGAS6180)Mutation(s): 0 
Find proteins for Q48UA4 (Streptococcus pyogenes serotype M28 (strain MGAS6180))
Go to UniProtKB:  Q48UA4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
1GP
Query on 1GP

Download SDF File 
Download CCD File 
A, B
SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.650α = 90.00
b = 82.970β = 90.00
c = 130.360γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata scaling

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 Allergy and Infectious DiseasesUnited States1R21AI113253
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP30GM110787

Revision History 

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references
  • Version 1.2: 2019-04-17
    Type: Data collection, Database references