› 3pkc

X-ray diffraction
1.47Å resolution

M. tuberculosis MetAP with bengamide analog Y08, in Mn form

Released:
DOI: 10.2210/pdb3pkc/pdb
PDB entry 3pkc coloured by chain, front view.
PDB entry 3pkc coloured by chain, side view.
PDB entry 3pkc coloured by chain, top view.
Source organism: Mycobacterium tuberculosis
Primary publication:
Inhibition of Mycobacterium tuberculosis methionine aminopeptidases by bengamide derivatives.
Lu JP, Yuan XH, Yuan H, Wang WL, Wan B, Franzblau SG, Ye QZ
ChemMedChem 6 1041-8 (2011)
PMID: 21465667

Function and Biology Details

Reaction catalysed: 
Release of N-terminal amino acids, preferentially methionine, from peptides and arylamides.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-161719 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Methionine aminopeptidase 2 Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 30.92 KDa
Source organism: Mycobacterium tuberculosis
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WK19 (Residues: 1-285; Coverage: 100%)
Gene names: MTV003.07c, Rv2861c, map, mapB
Sequence domains: Metallopeptidase family M24
Structure domains: Creatinase/methionine aminopeptidase superfamily

Ligands and Environments

2 bound ligands:
Ligand MN 2 x MN
Ligand Y08 1 x Y08
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: C2
Unit cell:
a: 57.667Å b: 79.945Å c: 65.055Å
α: 90° β: 91.8° γ: 90°
R-values:
R R work R free
0.186 0.184 0.216
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Chemistry and biology of bengamides and bengazoles, bioactive natural products from Jaspis sponges.
García-Ruiz et al. (2014)
3 more

3 mentions without citation

Advances in Bacterial Methionine Aminopeptidase Inhibition.
Helgren et al. (2016)
2 more