1OD1

Endothiapepsin PD135,040 complex

• PDB DOI: https://doi.org/10.2210/pdb1OD1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Cryphonectria parasitica
• Mutation(s): No 


• Deposited: 2003-02-12 Released: 2003-06-12 
• Deposition Author(s): Coates, L., Erskine, P.T., Mall, S., Gill, R.S., Wood, S.P., Cooper, J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.159 
• R-Value Observed: 0.125 

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 D Biol Crystallogr 59: 978

• PubMed: 12777758 
• DOI: https://doi.org/10.1107/s0907444903006267
• Primary Citation of Related Structures:  
  1OD1


• 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 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.

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Organizational Affiliation: 

School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, England. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.79 kDa 
• Atom Count: 2,913 
• Modelled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOTHIAPEPSIN	A	330	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0QS	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
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000361 (0QS)	B [auth A]	GEM-DIOL INHIBITOR PD-135.040	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.159 
• R-Value Observed: 0.125 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.201	α = 90
b = 73.249	β = 110.1
c = 45.993	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-12 
Deposition Author(s): Coates, L., Erskine, P.T., Mall, S., Gill, R.S., Wood, S.P., Cooper, J.B.

Revision History  

• Version 1.0: 2003-06-12
  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: 2012-11-30
  Changes: Other
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary