› 4wye

X-ray diffraction
1.75Å resolution

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis complexed with a DSF fragment hit

Released:
DOI: 10.2210/pdb4wye/pdb
PDB entry 4wye coloured by chain, front view.
PDB entry 4wye coloured by chain, side view.
PDB entry 4wye coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Fragment-based exploration of binding site flexibility in Mycobacterium tuberculosis BioA.
Dai R, Geders TW, Liu F, Park SW, Schnappinger D, Aldrich CC, Finzel BC
J Med Chem 58 5208-17 (2015)
PMID: 26068403

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + 8-amino-7-oxononanoate = S-adenosyl-4-methylthio-2-oxobutanoate + 7,8-diaminononanoate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-162055 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 457 amino acids
Theoretical weight: 48.54 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WQ81 (Residues: 1-437; Coverage: 100%)
Gene names: MTCY336.35c, Rv1568, bioA
Sequence domains: Aminotransferase class-III
Structure domains:

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
4 bound ligands:
Ligand 3VW 2 x 3VW
Ligand EPE 2 x EPE
Ligand SO4 1 x SO4
Ligand ACN 1 x ACN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P212121
Unit cell:
a: 62.692Å b: 66.249Å c: 202.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.206
Expression system: Escherichia coli

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Citations

3 review citations

Theory and applications of differential scanning fluorimetry in early-stage drug discovery.
Gao et al. (2020)
2 more

1 mention without citation

Fragment-based exploration of binding site flexibility in Mycobacterium tuberculosis BioA.
Dai et al. (2015)