6RON | pdb_00006ron

Endothiapepsin in complex with compound 046

• PDB DOI: https://doi.org/10.2210/pdb6RON/pdb

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


• Deposited: 2019-05-13 Released: 2020-07-08 
• Deposition Author(s): Magari, F., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.153 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

Endothiapepsin in complex with compound 046

Magari, F., Heine, A., Konstantinidou, M., Sutanto, F., Haupenthal, J., Jumde, R.V., Unver, M.Y., Camacho, C.J., Hirsch, A.K.H., Doemling, 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: 34.48 kDa 
• Atom Count: 2,811 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KCE (Subject of Investigation/LOI)	B [auth A]	[(1~{S},2~{R})-1-[1-(1,3-benzodioxol-5-ylmethyl)-1,2,3,4-tetrazol-5-yl]-3-(4-~{tert}-butylphenyl)-2-methyl-propyl]diazane C23 H30 N6 O2 BBOIZOIQFPNBML-VFNWGFHPSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A], E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free:  0.153 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.130 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.764	α = 90
b = 73.352	β = 109.65
c = 53.175	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Magari, F., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary