2VS2

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


Experimental Data Snapshot

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 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:  

  • 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. B ...

    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 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOTHIAPEPSIN
A
330Cryphonectria parasiticaMutation(s): 0 
Gene Names: EAPA (EPN-1)
EC: 3.4.23.22
Find proteins for P11838 (Cryphonectria parasitica)
Go to UniProtKB:  P11838
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QS
Query on 0QS

Download SDF File 
Download CCD File 
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
PD-135,040
C36 H56 F2 N7 O8 S
RRJUDVVMLCYZDV-DTXPUJKBSA-O
 Ligand Interaction
DOD
Query on DOD

Download SDF File 
Download CCD File 
A
DEUTERATED WATER
D2 O
XLYOFNOQVPJJNP-ZSJDYOACSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000361 (0QS)
Query on PRD_000361
AGEM-DIOL INHIBITOR PD-135.040Peptide-like / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SUI
Query on SUI
A
L-PEPTIDE LINKINGC6 H8 N2 O4ASP, GLY
Experimental Data & Validation

Experimental Data

  • Method: NEUTRON DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.219 
Software Package:
Software NamePurpose
MOLREPphasing
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2013-03-06
    Type: Other
  • Version 1.3: 2013-09-25
    Type: Database references, Other
  • Version 1.4: 2014-07-16
    Type: Advisory, Other, Structure summary
  • Version 1.5: 2017-03-22
    Type: Data collection
  • Version 1.6: 2017-07-12
    Type: Refinement description
  • Version 1.7: 2018-11-14
    Type: Data collection