4Y4U

Endothiapepsin in complex with fragment 14

• PDB DOI: https://doi.org/10.2210/pdb4Y4U/pdb

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


• Deposited: 2015-02-11 Released: 2016-03-02 
• Deposition Author(s): Radeva, N., Uehlein, M., Weiss, M.S., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.189 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 

Starting Model: experimental

Literature

Crystallographic Fragment Screening of an Entire Library

Radeva, N., 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: 34.44 kDa 
• Atom Count: 2,755 
• 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
46V	E [auth A]	1-(4-bromo-2-chlorophenyl)-3-methylthiourea C8 H8 Br Cl N2 S LXSVLJOSFCRPPA-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.189 
• R-Value Work: 0.155 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.599	α = 90
b = 72.823	β = 108.86
c = 52.732	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
HKL-2000	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Radeva, N., Uehlein, M., Weiss, M.S., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary