4M2X

Mycobacterium tuberculosis dihydrofolate reductase complexed with trimetrexate (TMQ)

• PDB DOI: https://doi.org/10.2210/pdb4M2X/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-05 Released: 2014-11-12 
• Deposition Author(s): Jung, H., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 

Literature

Selective inhibitors for dihydrofolate reductase from mycobacterium tuberculosis

Jung, H., Sacchettini, J.C.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.63 kDa 
• Atom Count: 5,467 
• Modelled Residue Count: 636 
• Deposited Residue Count: 648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B [auth C], C [auth E], D [auth G]	162	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: folA, dfrA, Rv2763c, MT2833, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	DA [auth G], E [auth A], N [auth C], V [auth E]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TMQ	EA [auth G], F [auth A], O [auth C], W [auth E]	TRIMETREXATE C19 H24 N5 O3 NOYPYLRCIDNJJB-UHFFFAOYSA-O
PO4	M [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	AA [auth E], BA [auth E], CA [auth E], FA [auth G], G [auth A], GA [auth G], H [auth A], HA [auth G], I [auth A], IA [auth G], J [auth A], K [auth A], L [auth A], P [auth C], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], X [auth E], Y [auth E], Z [auth E]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.261 
• R-Value Work: 0.197 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.09	α = 93.48
b = 64.838	β = 94.1
c = 68.062	γ = 100.25

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Jung, H., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations