Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 34841.07 
• Atom Count: 2462 
• Residue Count: 338 
• Unique protein chains: 2

1ER8

THE ACTIVE SITE OF ASPARTIC PROTEINASES

• DOI: 10.2210/pdb1ER8/pdb

• Classification: HYDROLASE
• Organism(s): Cryphonectria parasitica, Equus caballus


• 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 Å
• R-Value Work: 0.170 

Literature

The Active Site of Aspartic Proteinases

Pearl, L., Blundell, T.

(1984) FEBS Lett. 174: 96-101

• PubMed: 6381096 
• Primary Citation of Related Structures:  
  4ER2, 4ER1, 4APE, 3ER3


• 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.

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Related Citations: 

• Four-Fold Structural Repeat in the Acid Proteases
  Blundell, T.L.,Sewell, B.T.,Mclachlan, A.D.
  (1979) Biochim.Biophys.Acta 580: 24
• The Three-Dimensional Structure of Acid Proteinases
  Blundell, T.L.,Jenkins, J.A.,Khan, G.,Roychowdhury, P.,Sewell, T.,Tickle, I.J.,Wood, E.A.
  (1979) Proc.FEBS Meet. 52: 81
• X-Ray Analysis and Circular Dichroism of the Acid Protease from Endothia Parasitica and Chymosin
  Jenkins, J.,Tickle, I.,Sewell, T.,Ungaretti, L.,Wollmer, A.,Blundell, T.
  (1977) Adv.Exp.Med.Biol. 95: 43
• Active Site of Acid Proteinases
  Blundell, T.L.,Jones, H.B.,Khan, G.,Taylor, G.,Sewell, T.S.,Pearl, L.H.,Wood, S.P.
  (1979) Proc.FEBS Meet. 60: 281
• Structural Evidence for Gene Duplication in the Evolution of Acid Proteases
  Tang, J.,James, M.N.G.,Hsu, I.N.,Jenkins, J.A.,Blundell, T.L.
  (1978) Nature 271: 618
• Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
  Subramanian, E.,Swan, I.D.A.,Liu, M.,Davies, D.R.,Jenkins, J.A.,Tickle, I.J.,Blundell, T.L.
  (1977) Proc.Natl.Acad.Sci.USA 74: 556

Macromolecules

Find similar proteins by: Sequence  |  Structure

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
H-77	I	8	Equus caballus	Mutation(s): 0  Gene Names: AGT (SERPINA8)
Find proteins for P01016 (Equus caballus) Go to Gene View: AGT Go to UniProtKB:  P01016

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHI	I	D-PEPTIDE LINKING	C6 H10 N3 O2		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 43.200	α = 90.00
b = 75.700	β = 97.10
c = 42.900	γ = 90.00

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1989-10-16 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other