6ZZ2 | pdb_00006zz2

Cocktail experiment E: fragments 52, 58, and 63 at 90 mM concentration in complex with Endothiapepsin

• PDB DOI: https://doi.org/10.2210/pdb6ZZ2/pdb

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


• Deposited: 2020-08-03 Released: 2021-08-11 
• Deposition Author(s): Hassaan, E., Klebe, G., Heine, A., Schiebel, J., Koester, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 
  0.145 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 
  0.127 (Depositor) 

Starting Model: experimental

Literature

Cocktail experiment E: fragments 52, 58, and 63 at 90 mM concentration in complex with Endothiapepsin

Hassaan, E., Klebe, G., Heine, A., Schiebel, J., Koester, H., Softley, C., Sattler, M.

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: 43.89 kDa 
• Atom Count: 2,788 
• Modeled Residue Count: 330 
• Deposited Residue Count: 419 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A	419	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
F63 (Subject of Investigation/LOI)	B [auth A]	N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine C11 H12 N2 O2 MUKCVLFJCGZPKF-UHFFFAOYSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A], F [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:  0.145 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.126 (DCC) 
• R-Value Observed: 0.127 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.401	α = 90
b = 73.178	β = 109.762
c = 52.659	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XSCALE	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Hassaan, E., Klebe, G., Heine, A., Schiebel, J., Koester, H.

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary