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› 6yt1

X-ray diffraction
1.9Å resolution

Mtb TMK crystal structure in complex with compound 26

Released:
DOI: 10.2210/pdb6yt1/pdb
Model geometry
Fit model/data
PDB entry 6yt1 coloured by chain, front view.
PDB entry 6yt1 coloured by chain, side view.
PDB entry 6yt1 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Endeavors towards transformation of M. tuberculosis thymidylate kinase (MtbTMPK) inhibitors into potential antimycobacterial agents.
Jian Y, Merceron R, De Munck S, Forbes HE, Hulpia F, Risseeuw MDP, Van Hecke K, Savvides SN, Munier-Lehmann H, Boshoff HIM, Van Calenbergh S
Eur J Med Chem 206 112659 (2020)
PMID: 32823003

Function and Biology Details

Reaction catalysed: 
[dTMP + ATP = dTDP + ADP., dTMP + ATP = dTDP + ADP.]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161736 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Thymidylate kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 214 amino acids
Theoretical weight: 22.66 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WKE1 (Residues: 1-214; Coverage: 100%)
Gene names: Rv3247c, tmk
Sequence domains: Thymidylate kinase

Ligands and Environments

2 bound ligands:
Ligand PK5 2 x PK5
Ligand CIT 3 x CIT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P43212
Unit cell:
a: 87.74Å b: 87.74Å c: 112.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.169 0.167 0.203
Expression system: Escherichia coli

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Citations

1 review citation

Targeting Mycobacterium tuberculosis iron-scavenging tools: a recent update on siderophores inhibitors.
Kumar et al. (2023)
1 other article

1 mention without 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)