9G4O | pdb_00009g4o

The strucuture of Streptococcus pyogenes GacA in complex with a fragment

• PDB DOI: https://doi.org/10.2210/pdb9G4O/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptococcus pyogenes
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-16 Released: 2025-07-30 
• Deposition Author(s): Yan, K., Dorfmueller, H.
• Funding Organization(s): Wellcome Trust, Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus

Yan, K., Stanley, M., Raimi, O., Kowalski, B., Gurvic, D., Grillenberger, S., Chen, X., Ferenbach, A.T., Dorfmueller, H., van Aalten, D.M.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 33.6 kDa 
• Atom Count: 2,523 
• Modeled Residue Count: 288 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose reductase	A	289	Streptococcus pyogenes	Mutation(s): 0  Gene Names: rmlD, SPy_0784 EC: 1.1.1.133
UniProt
Find proteins for Q9A0G6 (Streptococcus pyogenes serotype M1) Explore Q9A0G6  Go to UniProtKB:  Q9A0G6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	D [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
A1IH7 (Subject of Investigation/LOI)	E [auth A]	2-[4-(hydroxymethyl)phenyl]ethanoic acid C9 H10 O3 FWZBPBKAANKOJQ-UHFFFAOYSA-N
MPD	B [auth A], C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.155	α = 113.3
b = 45.702	β = 99.54
c = 48.44	γ = 95.01

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Yan, K., Dorfmueller, H.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	225350/Z/22/Z
Medical Research Council (MRC, United Kingdom)	United Kingdom	MR/V001094/1

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release