2VS2

Neutron diffraction structure of endothiapepsin in complex with a gem- diol inhibitor.

Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history. 


Literature

The Catalytic Mechanism of an Aspartic Proteinase Explored with Neutron and X-Ray Diffraction

Coates, L., Tuan, H.-F., Tomanicek, S., Kovalevsky, A., Mustyakimov, M., Erskine, P., Cooper, J.

(2008) J Am Chem Soc 130: 7235

  • DOI: 10.1021/ja801269x
  • Primary Citation of Related Structures:  
    2JJI, 2JJJ, 2VS2

  • PubMed Abstract: 

    • Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin ...

    Hydrogen atoms play key roles in enzyme mechanism, but as this study shows, even high-quality X-ray data to a resolution of 1 A cannot directly visualize them. Neutron diffraction, however, can locate deuterium atoms even at resolutions around 2 A. Both neutron and X-ray diffraction data have been used to investigate the transition state of the aspartic proteinase endothiapepsin. The different techniques reveal a different part of the story, revealing the clearest picture yet of the catalytic mechanism by which the enzyme operates. Room temperature neutron and X-ray diffraction data were used in a newly developed joint refinement software package to visualize deuterium atoms within the active site of the enzyme when a gem-diol transition state analogue inhibitor is bound at the active site. These data were also used to estimate their individual occupancy, while analysis of the differences between the bond lengths of the catalytic aspartates was performed using atomic resolution X-ray data. The two methods are in agreement on the protonation state of the active site with a transition state analogue inhibitor bound confirming the catalytic mechanism at which the enzyme operates.

    Related Citations: 
    • Preliminary Neutron and Ultrahigh-Resolution X-Ray Diffraction Studies of the Aspartic Proteinase Endothiapepsin Cocrystallized with a Gem-Diol Inhibitor.
      Tuan, H.-F., Erskine, P., Langan, P., Cooper, J., Coates, L.
      (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 1080
    Organizational Affiliation: 

    Spallation Neutron Source, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENDOTHIAPEPSINA329Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPA, EPN-1
EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica)
Explore P11838 
Go to UniProtKB:  P11838
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11838
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QS
Query on 0QS
Download Ideal Coordinates CCD File 
B [auth A]N~2~-[(2R)-2-benzyl-3-(tert-butylsulfonyl)propanoyl]-N-{(1R)-1-(cyclohexylmethyl)-3,3-difluoro-2,2-dihydroxy-4-[(2-morpholin-4-ylethyl)amino]-4-oxobutyl}-3-(1H-imidazol-3-ium-4-yl)-L-alaninamide
C36 H56 F2 N7 O8 S
RRJUDVVMLCYZDV-DTXPUJKBSA-O		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SUI
Query on SUI		A L-PEPTIDE LINKINGC6 H8 N2 O4ASP, GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000361 (0QS)
Query on PRD_000361		B [auth A]GEM-DIOL INHIBITOR PD-135.040Peptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.03α = 90
b = 75.72β = 97.02
c = 42.97γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-27
    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: 2013-03-06
    Changes: Other
  • Version 1.3: 2013-09-25
    Changes: Database references, Other
  • Version 1.4: 2014-07-16
    Changes: Advisory, Other, Structure summary
  • Version 1.5: 2017-03-22
    Changes: Data collection
  • Version 1.6: 2017-07-12
    Changes: Refinement description
  • Version 1.7: 2018-11-14
    Changes: Data collection