7KM7 | pdb_00007km7

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, tetragonal crystal from

• PDB DOI: https://doi.org/10.2210/pdb7KM7/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Mycobacterium ulcerans Agy99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-02 Released: 2021-07-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, tetragonal crystal form

Abendroth, J., Dranow, D.M., 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

Macromolecule Content 

• Total Structure Weight: 20.41 kDa 
• Atom Count: 1,463 
• Modeled Residue Count: 158 
• 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): 1  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	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
WPD (Subject of Investigation/LOI)	C [auth A]	(2S)-2-[(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid C19 H24 F2 N4 O4 QMHPAIITCHQDEY-CYBMUJFWSA-N
BR	D [auth A], E [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37km7

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.13	α = 90
b = 59.13	β = 90
c = 129.49	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-07-07
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description