1GVX

Endothiapepsin complexed with H256


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.166 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Five Atomic Resolution Structures of Endothiapepsin Inhibitor Complexes: Implications for the Aspartic Proteinase Mechanism

Coates, L.Erskine, P.T.Crump, M.P.Wood, S.P.Cooper, J.B.

(2002) J Mol Biol 318: 1405

  • DOI: 10.1016/s0022-2836(02)00197-3
  • Primary Citation of Related Structures:  
    1GVW, 1GVV, 1GVU, 1GVT, 1GVX

  • PubMed Abstract: 
  • Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond ...

    Endothiapepsin is derived from the fungus Endothia parasitica and is a member of the aspartic proteinase class of enzymes. This class of enzyme is comprised of two structurally similar lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The three-dimensional structures of endothiapepsin bound to five transition state analogue inhibitors (H189, H256, CP-80,794, PD-129,541 and PD-130,328) have been solved at atomic resolution allowing full anisotropic modelling of each complex. The active sites of the five structures have been studied with a view to studying the catalytic mechanism of the aspartic proteinases by locating the active site protons by carboxyl bond length differences and electron density analysis. In the CP-80,794 structure there is excellent electron density for the hydrogen on the inhibitory statine hydroxyl group which forms a hydrogen bond with the inner oxygen of Asp32. The location of this proton has implications for the catalytic mechanism of the aspartic proteinases as it is consistent with the proposed mechanism in which Asp32 is the negatively charged aspartate. A number of short hydrogen bonds (approximately 2.6 A) with ESD values of around 0.01 A that may have a role in catalysis have been identified within the active site of each structure; the lengths of these bonds have been confirmed using NMR techniques. The possibility and implications of low barrier hydrogen bonds in the active site are considered.


    Organizational Affiliation

    School of Biological Sciences, University of Southampton, UK. leightonc@bigfoot.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOTHIAPEPSINA329Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPAEPN-1
EC: 3.4.23.22
Find proteins for P11838 (Cryphonectria parasitica)
Explore P11838 
Go to UniProtKB:  P11838
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
INHIBITOR H256B [auth I]6synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SUI
Query on SUI
AL-PEPTIDE LINKINGC6 H8 N2 O4ASP, GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.166 
  • R-Value Observed: 0.140 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.881α = 90
b = 75.446β = 97.47
c = 43.226γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2011-12-07
    Changes: Atomic model, Other
  • Version 1.3: 2013-03-06
    Changes: Other
  • Version 1.4: 2016-12-21
    Changes: Atomic model, Data collection, Derived calculations, Other, Source and taxonomy, Structure summary