6SCV | pdb_00006scv

Endothiapepsin in complex with ligand 69

• PDB DOI: https://doi.org/10.2210/pdb6SCV/pdb

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


• Deposited: 2019-07-25 Released: 2020-08-26 
• Deposition Author(s): Magari, F., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

Literature

Endothiapepsin in complex with ligand 69

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: 34.21 kDa 
• Atom Count: 2,704 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L7K (Subject of Investigation/LOI)	C [auth A]	[(~{R})-cyclohexyl-[1-(2-phenylethyl)-1,2,3,4-tetrazol-5-yl]methyl]diazane C16 H24 N6 RYAQXBFFYZPWMF-OAHLLOKOSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.283	α = 90
b = 73.04	β = 109.378
c = 52.878	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Magari, F., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Structure summary