4YD3 | pdb_00004yd3

Endothiapepsin in complex with fragment 224

• PDB DOI: https://doi.org/10.2210/pdb4YD3/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: 1.25 Å
• R-Value Free: 
  0.132 (Depositor), 0.130 (DCC) 
• R-Value Work: 
  0.111 (Depositor) 
• R-Value Observed: 
  0.112 (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: 35.32 kDa 
• Atom Count: 2,896 
• 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
4AQ	B [auth A], C [auth A]	2-(1H-indol-3-yl)-N-[(1-methyl-1H-pyrrol-2-yl)methyl]ethanamine C16 H19 N3 JMDFJNUSALBEDM-UHFFFAOYSA-N
1PE	L [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PEG	M [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ACT	J [auth A], K [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.132 (Depositor), 0.130 (DCC) 
• R-Value Work:  0.111 (Depositor) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.339	α = 90
b = 73.242	β = 109.68
c = 52.728	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: 2024-10-09
  Changes: Structure summary