3URI

Endothiapepsin-DB5 complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

An analysis of subdomain orientation, conformational change and disorder in relation to crystal packing of aspartic proteinases.

Bailey, D.Carpenter, E.P.Coker, A.Coker, S.Read, J.Jones, A.T.Erskine, P.Aguilar, C.F.Badasso, M.Toldo, L.Rippmann, F.Sanz-Aparicio, J.Albert, A.Blundell, T.L.Roberts, N.B.Wood, S.P.Cooper, J.B.

(2012) Acta Crystallogr D Biol Crystallogr 68: 541-552

  • DOI: 10.1107/S0907444912004817
  • Primary Citation of Related Structures:  
    3URI, 3URJ, 3URL, 3UTL

  • PubMed Abstract: 
  • The analysis reported here describes detailed structural studies of endothiapepsin (the aspartic proteinase from Endothia parasitica), with and without bound inhibitors, and human pepsin 3b. Comparison of multiple crystal structures of members of the aspartic proteinase family has revealed small but significant differences in domain orientation in different crystal forms ...

    The analysis reported here describes detailed structural studies of endothiapepsin (the aspartic proteinase from Endothia parasitica), with and without bound inhibitors, and human pepsin 3b. Comparison of multiple crystal structures of members of the aspartic proteinase family has revealed small but significant differences in domain orientation in different crystal forms. In this paper, it is shown that these differences in domain orientation do not necessarily correlate with the presence or absence of bound inhibitors, but appear to stem at least partly from crystal contacts mediated by sulfate ions. However, since the same inherent flexibility of the structure is observed for other enzymes in this family such as human pepsin, the native structure of which is also reported here, the observed domain movements may well have implications for the mechanism of catalysis.


    Organizational Affiliation

    Incisive Media, 32-34 Broadwick Street, London W1A 2HG, England.



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
UniProt
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
DB5 peptideB8N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SUI
Query on SUI
AL-PEPTIDE LINKINGC6 H8 N2 O4ASP, GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000855
Query on PRD_000855
BDB5 peptidePeptide-like /  Enzyme inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.02α = 90
b = 75.56β = 97.02
c = 42.8γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
FFTmodel building
SHELXL-97refinement
Cadraldata reduction
ROTAVATAdata scaling
FFTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references
  • Version 1.2: 2012-05-09
    Changes: Database references
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2015-12-16
    Changes: Atomic model
  • Version 1.5: 2017-11-08
    Changes: Refinement description
  • Version 1.6: 2018-04-18
    Changes: Data collection