3Q6Y | pdb_00003q6y

Endothiapepsin in complex with a pyrrolidine based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3Q6Y/pdb

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


• Deposited: 2011-01-04 Released: 2012-01-04 
• Deposition Author(s): Koester, H., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.184 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Endothiapepsin in complex with a pyrrolidine based inhibitor

Koester, H., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 34.75 kDa 
• Atom Count: 2,572 
• Modeled Residue Count: 305 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S47	C [auth A]	(3S,4S)-pyrrolidine-3,4-diyl bis(naphthalen-1-ylacetate) C28 H25 N O4 ATWKPWWBTFNYMB-UIOOFZCWSA-N
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.184 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.36	α = 90
b = 72.79	β = 108.6
c = 51.79	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Koester, H., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary