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 

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.,Sect.D 68: 541-552

  • DOI: 10.1107/S0907444912004817
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pepsin A
A
326Homo sapiensMutation(s): 0 
Gene Names: PGA4
EC: 3.4.23.1
Find proteins for P0DJD7 (Homo sapiens)
Go to Gene View: PGA4
Go to UniProtKB:  P0DJD7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.890α = 90.00
b = 75.270β = 90.00
c = 87.100γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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