1OD1

Endothiapepsin PD135,040 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structure of Endothiapepsin Complexed with the Gem-Diol Inhibitor Pd-135,040 at 1.37 A

Coates, L.Erskine, P.T.Mall, S.Williams, P.A.Gill, R.S.Wood, S.P.Cooper, J.B.

(2003) Acta Crystallogr.,Sect.D 59: 978


  • PubMed Abstract: 
  • The crystal structure of endothiapepsin complexed with the gem-diol inhibitor PD-135,040 has been anisotropically refined to a resolution of 1.37 A. The structure of this inhibitor complex is in agreement with previous structures of endothiapepsin ge ...

    The crystal structure of endothiapepsin complexed with the gem-diol inhibitor PD-135,040 has been anisotropically refined to a resolution of 1.37 A. The structure of this inhibitor complex is in agreement with previous structures of endothiapepsin gem-diol inhibitor complexes that have been used to develop proposed catalytic mechanisms. However, the increase in resolution over previous structures confirms the presence of a number of short hydrogen bonds within the active site that are likely to play an important role in the catalytic mechanism. The presence of low-barrier hydrogen bonds was indicated in a previous one-dimensional H NMR spectrum.


    Organizational Affiliation

    School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, England. leightonc@bigfoot.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDOTHIAPEPSIN
A
330Cryphonectria parasiticaGene 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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000361 (0QS)
Query on PRD_000361
AGEM-DIOL INHIBITOR PD-135.040Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 53.201α = 90.00
b = 73.249β = 110.10
c = 45.993γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-12
    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: 2012-11-30
    Type: Other