3DYB

proteinase K- digalacturonic acid complex

Summary for 3DYB

• Entry DOI: 10.2210/pdb3dyb/pdb
• Descriptor: Proteinase K, alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: proteinase k, hepes, digalacturonic acid, silverbullets, structural genomics, psi-2, protein structure initiative, center for high-throughput structural biology, chtsb, hydrolase, metal-binding, protease, serine protease, zymogen
• Biological source: Engyodontium album (Engyodontium album)
• Total number of polymer chains: 1
• Total formula weight: 29647.51

Authors

Larson, S.B.,Day, J.S.,McPherson, A.,Cudney, R.,Nguyen, C.,Center for High-Throughput Structural Biology (CHTSB) (deposition date: 2008-07-25, release date: 2008-10-07, Last modification date: 2024-11-13)

Primary citation

Larson, S.B.,Day, J.S.,Nguyen, C.,Cudney, R.,McPherson, A.
High-resolution structure of proteinase K cocrystallized with digalacturonic acid.
Acta Crystallogr.,Sect.F, 65:192-198, 2009

PubMed Abstract: Proteinase K, a subtilisin-like fungal protease, was crystallized from a cocktail of small molecules containing digalacturonic acid (DGA). The crystal structure was determined to 1.32 A resolution and refined to an R factor of 0.158. The final model contained, beside the protein, two calcium ions, 379 water molecules, a molecule of DGA and a partially occupied HEPES molecule. The DGA molecule has one sugar moiety disposed exactly on a crystallographic twofold axis; the second ring was not observed. The DGA molecule is bound to two protein molecules across the twofold axis through hydrogen-bonding networks involving Ser150 and water molecules. One of the calcium-ion sites has not been reported previously. This study further illustrates the involvement of small molecules in the crystallization of macromolecules through their ability to form intermolecular lattice interactions.

PubMed: 19255463
DOI: 10.1107/S1744309109002218

Experimental method

X-RAY DIFFRACTION (1.32 Å)