3ER3

The active site of aspartic proteinases

Summary for 3ER3

• Entry DOI: 10.2210/pdb3er3/pdb
• Related PRD ID: PRD_000263
• Descriptor: ENDOTHIAPEPSIN, 6-ammonio-N-[(2R,4R,5R)-5-{[N-(tert-butoxycarbonyl)-L-phenylalanyl-3-(1H-imidazol-3-ium-4-yl)-L-alanyl]amino}-6-cyclohexyl-4-hydroxy-2-(2-methylpropyl)hexanoyl]-L-norleucylphenylalanine (3 entities in total)
• Functional Keywords: acid proteinase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Cryphonectria parasitica (chestnut blight fungus)
• Total number of polymer chains: 1
• Total formula weight: 34761.07

Authors

Al-Karadaghi, S.,Cooper, J.B.,Veerapandian, B.,Hoover, D.,Blundell, T.L. (deposition date: 1991-01-02, release date: 1991-04-15, Last modification date: 2024-10-23)

Primary citation

Pearl, L.,Blundell, T.
The Active Site of Aspartic Proteinases
FEBS Lett., 174:96-101, 1984

PubMed Abstract: The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.

PubMed: 6381096
DOI: 10.1016/0014-5793(84)81085-6

Experimental method

X-RAY DIFFRACTION (2 Å)