› 6vsd

X-ray diffraction
1.69Å resolution

Mycobacterium tuberculosis dihydrofolate reductase in complex with 3-((thiophen-2-ylthio)methyl)benzoic acid (fragment 13)

Released:
DOI: 10.2210/pdb6vsd/pdb
PDB entry 6vsd coloured by chain, front view.
PDB entry 6vsd coloured by chain, side view.
PDB entry 6vsd coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase from Mycobacterium tuberculosis.
Ribeiro JA, Hammer A, Libreros-Zúñiga GA, Chavez-Pacheco SM, Tyrakis P, de Oliveira GS, Kirkman T, El Bakali J, Rocco SA, Sforça ML, Parise-Filho R, Coyne AG, Blundell TL, Abell C, Dias MVB
ACS Infect Dis 6 2192-2201 (2020)
PMID: 32603583

Function and Biology Details

Reaction catalysed: 
5,6,7,8-tetrahydrofolate + NADP(+) = 7,8-dihydrofolate + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161902 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dihydrofolate reductase Chains: A, B
Molecule details ›
Chains: A, B
Length: 161 amino acids
Theoretical weight: 17.89 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WNX1 (Residues: 1-161; Coverage: 100%)
Gene names: MTV002.28c, Rv2763c, dfrA, folA
Sequence domains: Dihydrofolate reductase

Ligands and Environments


Cofactor: Ligand NAP 2 x NAP
4 bound ligands:
Ligand JBB 2 x JBB
Ligand CO 2 x CO
Ligand SO4 1 x SO4
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: LNLS BEAMLINE W01B-MX2
Spacegroup: P212121
Unit cell:
a: 61.745Å b: 71.171Å c: 71.798Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.21
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis.
Mori et al. (2021)
3 other articles

3 mentions without citation

Active components in Ephedra sinica stapf disrupt the interaction between ACE2 and SARS-CoV-2 RBD: Potent COVID-19 therapeutic agents.
Mei et al. (2021)
2 more