› 6p63

X-ray diffraction
2.4Å resolution

Wild-type NIS synthetase DesD bound to AMP and substrate analog cadaverine

Released:
DOI: 10.2210/pdb6p63/pdb
PDB entry 6p63 coloured by chain, front view.
PDB entry 6p63 coloured by chain, side view.
PDB entry 6p63 coloured by chain, top view.
Source organism: Streptomyces coelicolor
Primary publication:
Cofactor Complexes of DesD, a Model Enzyme in the Virulence-related NIS Synthetase Family.
Hoffmann KM, Goncuian ES, Karimi KL, Amendola CR, Mojab Y, Wood KM, Prussia GA, Nix J, Yamamoto M, Lathan K, Orion IW
Biochemistry 59 3427-3437 (2020)
PMID: 32885650

Function and Biology Details

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-192185 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Siderophore Synthetase Type C DesD Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 595 amino acids
Theoretical weight: 66.67 KDa
Source organism: Streptomyces coelicolor
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9L069 (Residues: 1-595; Coverage: 100%)
Gene names: SCC105.16, SCO2785, desD
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand AMP 4 x AMP
Ligand MG 4 x MG
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU R-AXIS IV
Spacegroup: P21
Unit cell:
a: 98.43Å b: 74.24Å c: 183.17Å
α: 90° β: 94.7° γ: 90°
R-values:
R R work R free
0.171 0.168 0.227
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Chemoenzymatic Synthesis of Select Intermediates and Natural Products of the Desferrioxamine E Siderophore Pathway.
Hoffmann et al. (2022)

1 mention without citation

An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD.
Yang et al. (2022)