› 5x9d

X-ray diffraction
2.1Å resolution

Crystal structure of homoserine dehydrogenase in complex with L-cysteine and NAD

Released:
DOI: 10.2210/pdb5x9d/pdb
PDB entry 5x9d coloured by chain, front view.
PDB entry 5x9d coloured by chain, side view.
PDB entry 5x9d coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Primary publication:
Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex.
Ogata K, Yajima Y, Nakamura S, Kaneko R, Goto M, Ohshima T, Yoshimune K
Sci Rep 8 5749 (2018)
PMID: 29636528

Function and Biology Details

Reaction catalysed: 
L-homoserine + NAD(P)(+) = L-aspartate 4-semialdehyde + NAD(P)H
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123819 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
homoserine dehydrogenase Chain: A
Molecule details ›
Chain: A
Length: 304 amino acids
Theoretical weight: 33.41 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F9VNG5 (Residues: 1-304; Coverage: 100%)
Gene names: ST1519, STK_15190, hom
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand 80F 1 x 80F
Ligand TLA 1 x TLA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: I41
Unit cell:
a: 106.171Å b: 106.171Å c: 56.874Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.239
Expression system: Escherichia coli BL21(DE3)

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Citations

3 citation in other articles

New inhibitors of homoserine dehydrogenase from Paracoccidioides brasiliensis presenting antifungal activity.
Bueno et al. (2019)
2 more

2 mentions without citation

Inhibition of homoserine dehydrogenase by formation of a cysteine-NAD covalent complex.
Ogata et al. (2018)
1 more