› 6ikg

X-ray diffraction
2.3Å resolution

Crystal structure of substrate-bound S9 peptidase (S514A mutant) from Deinococcus radiodurans

Released:
DOI: 10.2210/pdb6ikg/pdb
PDB entry 6ikg coloured by chain, front view.
PDB entry 6ikg coloured by chain, side view.
PDB entry 6ikg coloured by chain, top view.
Source organisms:
Primary publication:
Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.
Yadav P, Goyal VD, Gaur NK, Kumar A, Gokhale SM, Jamdar SN, Makde RD
J Biol Chem 294 89-100 (2019)
PMID: 30409909

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166892 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidase S9 prolyl oligopeptidase catalytic domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 656 amino acids
Theoretical weight: 72.71 KDa
Source organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RXY9 (Residues: 2-655; Coverage: 100%)
Gene name: DR_0165
Sequence domains:
MET-ALA-ALA Chains: E, F
Molecule details ›
Chains: E, F
Length: 3 amino acids
Theoretical weight: 291 Da
Source organism: Deinococcus radiodurans
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RRCAT INDUS-2 BEAMLINE PX-BL21
Spacegroup: P21
Unit cell:
a: 71.649Å b: 214.636Å c: 92.022Å
α: 90° β: 102.98° γ: 90°
R-values:
R R work R free
0.209 0.207 0.234
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 citation in other articles

The acid-base-nucleophile catalytic triad in ABH-fold enzymes is coordinated by a set of structural elements.
Denesyuk et al. (2020)
5 more

1 mention without citation

Carboxypeptidase in prolyl oligopeptidase family: Unique enzyme activation and substrate-screening mechanisms.
Yadav et al. (2019)