4YD4 | pdb_00004yd4

Endothiapepsin in complex with fragment 227

• PDB DOI: https://doi.org/10.2210/pdb4YD4/pdb

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


• Deposited: 2015-02-20 Released: 2016-03-02 
• Deposition Author(s): Stieler, M., Heine, A., Klebe, G.
• Funding Organization(s): BMBF

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.146 (Depositor), 0.148 (DCC) 
• R-Value Work: 
  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.123 (Depositor) 

Starting Model: experimental

Literature

Crystallographic Fragment Screening of an Entire Library

Stieler, M., 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: 34.81 kDa 
• Atom Count: 2,769 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4AY	F [auth A]	4-(bromomethyl)benzoic acid C8 H7 Br O2 CQQSQBRPAJSTFB-UHFFFAOYSA-N
PG4	J [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR	G [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.146 (Depositor), 0.148 (DCC) 
• R-Value Work:  0.121 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.123 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.342	α = 90
b = 73.49	β = 109.56
c = 53.026	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Stieler, M., Heine, A., Klebe, G.

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Funding Organization	Location	Grant Number
BMBF	Germany	05K13RM1

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: 2024-10-23
  Changes: Structure summary