4ER1

THE ACTIVE SITE OF ASPARTIC PROTEINASES

• PDB DOI: https://doi.org/10.2210/pdb4ER1/pdb

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


• Deposited: 1990-10-14 Released: 1991-01-15 
• Deposition Author(s): Quail, J.W., Cooper, J.B., Szelke, M., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.143 

Literature

The active site of aspartic proteinases

Pearl, L., Blundell, T.

(1984) FEBS Lett 174: 96-101

• PubMed: 6381096 
• DOI: https://doi.org/10.1016/0014-5793(84)81085-6
• Primary Citation of Related Structures:  
  1ER8, 3ER3, 4APE, 4ER1, 4ER2


• PubMed Abstract: 
  

  The active site of the aspartic proteinase, endothiapepsin, has been defined by X-ray analysis and restrained least-squares refinement at 2.1 A resolution with a crystallographic agreement value of 0.16. The environments of the two catalytically important aspartyl groups are remarkably similar and the contributions of the NH2- and COOH-terminal domains to the catalytic centre are related by a local 2-fold axis. The carboxylates of the aspartyls share a hydrogen bond and have equivalent contacts to a bound water molecule or hydroxonium ion lying on the local diad. The main chains around 32 and 215 are connected by a novel interaction involving diad-related threonines. It is suggested that the two pKa values of the active site aspartyls arise from a structure not unlike that in maleic acid with a hydrogen-bonded intermediate species and a dicarboxylate characterised by electrostatic repulsions between the two negatively charged groups.

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: 34.63 kDa 
• Atom Count: 2,709 
• 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 [auth E]	330	Cryphonectria parasitica	Mutation(s): 0  EC: 3.4.23.6 (PDB Primary Data), 3.4.23.22 (UniProt)
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZP	B [auth E]	N-[(1R,2R,4R)-1-(cyclohexylmethyl)-2-hydroxy-6-methyl-4-{[(2R)-2-methylbutyl]carbamoyl}heptyl]-3-(1H-imidazol-3-ium-4-y l)-N~2~-[3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanoyl]-L-alaninamide C51 H68 N5 O4 SIGGSNKWBGJQQB-XNTVDALVSA-O

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000382 (0ZP)	B [auth E]	PD125967	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.143 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.1	α = 90
b = 75.8	β = 97
c = 43	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-01-15 
Deposition Author(s): Quail, J.W., Cooper, J.B., Szelke, M., Blundell, T.L.

Revision History  

• Version 1.0: 1991-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary