5UJF | pdb_00005ujf

Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound p218 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5UJF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-17 Released: 2017-02-01 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound p218 Inhibitor

Mayclin, S.J., Fairman, J.W., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.67 kDa 
• Atom Count: 1,272 
• Modeled Residue Count: 161 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	180	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: folA, dfrA, Rv2763c, MTV002.28c EC: 1.5.1.3
UniProt
Find proteins for P9WNX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNX1  Go to UniProtKB:  P9WNX1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMV	F [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	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.49	α = 90
b = 59.49	β = 90
c = 102.67	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-01 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description