› 3dyb

X-ray diffraction
1.32Å resolution

proteinase K- digalacturonic acid complex

Released:
DOI: 10.2210/pdb3dyb/pdb
PDB entry 3dyb coloured by chain, front view.
PDB entry 3dyb coloured by chain, side view.
PDB entry 3dyb coloured by chain, top view.
Source organism: Parengyodontium album
Primary publication:
High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
Larson SB, Day JS, Nguyen C, Cudney R, McPherson A
Acta Crystallogr Sect F Struct Biol Cryst Commun 65 192-8 (2009)
PMID: 19255463

Function and Biology Details

Reaction catalysed: 
Hydrolysis of keratin, and of other proteins with subtilisin-like specificity. Hydrolyzes peptide amides.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139275 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Proteinase K Chain: A
Molecule details ›
Chain: A
Length: 279 amino acids
Theoretical weight: 28.96 KDa
Source organism: Parengyodontium album
UniProt:
  • Canonical: P06873 (Residues: 106-384; Coverage: 76%)
Gene name: PROK
Sequence domains: Subtilase family
Structure domains: Peptidase S8/S53 domain

Ligands and Environments

Carbohydrate polymer : NEW Components: ADA
Carbohydrate polymer
2 bound ligands:
Ligand CA 2 x CA
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P43212
Unit cell:
a: 67.72Å b: 67.72Å c: 101.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.158 0.207

Quick links

Citations

1 citations in other articles

FragMAXapp: crystallographic fragment-screening data-analysis and project-management system.
Lima et al. (2021)

3 mentions without citation

Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM.
Heymann JB. (2019)
2 more