5U26 | pdb_00005u26

Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and p218 Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5U26/pdb

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


• Deposited: 2016-11-29 Released: 2016-12-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.192 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.19 kDa 
• Atom Count: 1,513 
• Modeled Residue Count: 166 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A	179	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  folA, folA_1, BN1213_03327, BN1303_00864, ERS007661_02580, ERS007663_03946, ERS007665_02766, ERS007741_00337, ERS013471_00736, ERS023446_01268, ERS024213_02711, ERS027644_04978, ERS027646_03318, ERS027653_04780, ERS027654_00299, ERS027656_00246, ERS027659_04151, ERS027661_03595, ERS027666_04095, ERS031537_04020, ERS124361_01473, RN05_2938 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
NAP	C [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	E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.192 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.05	α = 90
b = 66.98	β = 90
c = 77.26	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description