7K62

Crystal Structure of Dihydrofolate reductase from Mycobacterium kansasii in complex with NADP and inhibitor P218

• PDB DOI: https://doi.org/10.2210/pdb7K62/pdb

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


• Deposited: 2020-09-18 Released: 2021-03-17 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Crystal Structure of Dihydrofolate reductase from Mycobacterium kansasii in complex with NADP and inhibitor P218

Abendroth, J., Dranow, D.M., Santhakumar, V., Walpole, C., 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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 39.81 kDa 
• Atom Count: 2,861 
• Modelled Residue Count: 330 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	167	Mycobacterium kansasii	Mutation(s): 0  Gene Names: folA, BZL29_1474, BZL30_0350 EC: 1.5.1.3
UniProt
Find proteins for A0A653EQ34 (Mycobacterium kansasii) Go to UniProtKB:  A0A653EQ34

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MMV (Subject of Investigation/LOI)	D [auth A], G [auth B]	3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid C18 H24 N4 O4 VDGXZSSDCDPCRF-UHFFFAOYSA-N
EDO	E [auth A], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.216 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/m37k62

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.1	α = 90
b = 66.25	β = 90
c = 86.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-17 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-03-17
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description