4LAP | pdb_00004lap

Endothiapepsin in complex with thiophen-based inhibitor SAP114

• PDB DOI: https://doi.org/10.2210/pdb4LAP/pdb

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


• Deposited: 2013-06-20 Released: 2014-12-24 
• Deposition Author(s): Park, A., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Work: 
  0.129 (Depositor), 0.129 (DCC) 
• R-Value Observed: 
  0.130 (Depositor) 

Literature

Endothiapepsin in Complex with Thiophen based Inhibitors

Kuhnert, M., Park, A., Heine, A., Klebe, G., Diederich, W.E.

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: 34.45 kDa 
• Atom Count: 2,812 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1VT	B [auth A]	N-benzyl-2-[(N-benzyl-beta-alanyl)amino]-4-phenylthiophene-3-carboxamide C28 H27 N3 O2 S WYXRECOQBJBCCU-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Work:  0.129 (Depositor), 0.129 (DCC) 
• R-Value Observed: 0.130 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.419	α = 90
b = 73.064	β = 109.68
c = 52.752	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Park, A., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary