5SCV

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-889

• PDB DOI: https://doi.org/10.2210/pdb5SCV/pdb
• Deposition Group: G_1002223 (ground state) ExploreG_1002223

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


• Deposited: 2021-12-20 Released: 2022-02-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-889

Mayclin, S.J., Fairman, J.W., Dranow, D.M., Conrady, D.G., Fox III, D., Lukacs, C.M., Lorimer, D.D., Horanyi, P.S., Edwards, T.E., Abendroth, J.

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)

Macromolecule Content

• Total Structure Weight: 42.05 kDa 
• Atom Count: 3,146 
• Modelled Residue Count: 339 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	179	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
NAP	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
H4U (Subject of Investigation/LOI)	D [auth A], G [auth B]	6-ethyl-5-(4-{3-[3-(1H-tetrazol-5-yl)propyl]phenoxy}butoxy)pyrimidine-2,4-diamine C20 H28 N8 O2 QSPOUTDHJRMRRP-UHFFFAOYSA-N
CL	E [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.192 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.26	α = 90
b = 67.42	β = 96.42
c = 75.25	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2022-03-02
  Changes: Other, Structure summary