6UWW | pdb_00006uww

Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with P218 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6UWW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium ulcerans Agy99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-05 Released: 2020-11-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free: 
  0.145 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.132 (Depositor) 
• R-Value Observed: 
  0.132 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of dihydrofolate reductase from Mycobacterium ulcerans with SDDC-0001565 inhibitor

Mayclin, S.J., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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)

Macromolecule Content 

• Total Structure Weight: 20.39 kDa 
• Atom Count: 1,686 
• Modeled Residue Count: 163 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	173	Mycobacterium ulcerans Agy99	Mutation(s): 0  Gene Names: dfrA, MUL_2179 EC: 1.5.1.3
UniProt
Find proteins for A0PQG8 (Mycobacterium ulcerans (strain Agy99)) Explore A0PQG8  Go to UniProtKB:  A0PQG8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MMV	B [auth A]	3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid C18 H24 N4 O4 VDGXZSSDCDPCRF-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.92 Å
• R-Value Free:  0.145 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.132 (Depositor) 
• R-Value Observed: 0.132 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.73	α = 90
b = 66.2	β = 91.614
c = 44.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-11-11
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Structure summary