1ER8 | pdb_00001er8

THE ACTIVE SITE OF ASPARTIC PROTEINASES

• PDB DOI: https://doi.org/10.2210/pdb1ER8/pdb

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


• Deposited: 1989-10-16 Released: 1991-10-15 
• Deposition Author(s): Hemmings, A.M., Veerapandian, B., Szelke, M., Cooper, J.B., Blundell, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.170 (Depositor) 

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 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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.84 kDa 
• Atom Count: 2,529 
• Modeled Residue Count: 338 
• Deposited Residue Count: 338 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endothiapepsin	A [auth E]	330	Cryphonectria parasitica	Mutation(s): 0  Gene Names: EAPA, EPN-1 EC: 3.4.23.22
UniProt
Find proteins for P11838 (Cryphonectria parasitica) Explore P11838  Go to UniProtKB:  P11838

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H-77	B [auth I]	8	Equus caballus	Mutation(s): 0  Gene Names: AGT
UniProt
Find proteins for P01016 (Equus caballus) Explore P01016  Go to UniProtKB:  P01016

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.170 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.2	α = 90
b = 75.7	β = 97.1
c = 42.9	γ = 90

Structure Validation

Entry History 

Deposition Data

• Released Date: 1991-10-15 
Deposition Author(s): Hemmings, A.M., Veerapandian, B., Szelke, M., Cooper, J.B., Blundell, T.L.

Revision History  

• Version 1.0: 1991-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary