3UTL

Human pepsin 3b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 asp ...

    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
Pepsin A A326Homo sapiensMutation(s): 0 
Gene Names: PGA4
EC: 3.4.23.1
Find proteins for P0DJD7 (Homo sapiens)
Explore P0DJD7 
Go to UniProtKB:  P0DJD7
NIH Common Fund Data Resources
PHAROS:  P0DJD7
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.89α = 90
b = 75.27β = 90
c = 87.1γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references
  • Version 1.2: 2012-05-09
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description