The active site of aspartic proteinases

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Work: 0.186 

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This is version 1.4 of the entry. See complete history


The active site of aspartic proteinases

Pearl, L.Blundell, T.

(1984) FEBS Lett 174: 96-101

  • DOI: https://doi.org/10.1016/0014-5793(84)81085-6
  • Primary Citation of Related Structures:  
    1ER8, 3ER3, 4APE, 4ER1, 4ER2

  • 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.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ENDOTHIAPEPSINA [auth E]330Cryphonectria parasiticaMutation(s): 0 
Find proteins for P11838 (Cryphonectria parasitica)
Explore P11838 
Go to UniProtKB:  P11838
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11838
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PEPSTATINB [auth I]6Streptomyces argenteolus subsp. toyonakensisMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
Query on PRD_000557
B [auth I]PepstatinOligopeptide / Enzyme inhibitor
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.1α = 90
b = 75.6β = 97
c = 42.9γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1991-01-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2013-02-27
    Changes: Other
  • Version 1.4: 2017-11-29
    Changes: Derived calculations, Other