4LP9

Endothiapepsin complexed with Phe-reduced-Tyr peptide.

• PDB DOI: https://doi.org/10.2210/pdb4LP9/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Cryphonectria parasitica
• Mutation(s): No 


• Deposited: 2013-07-15 Released: 2014-01-15 
• Deposition Author(s): Guo, J., Cooper, J.B., Wood, S.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.165 
• R-Value Work: 0.123 
• R-Value Observed: 0.125 

Starting Model: experimental

Literature

The structure of endothiapepsin complexed with a Phe-Tyr reduced-bond inhibitor at 1.35 angstrom resolution.

Guo, J., Cooper, J.B., Wood, S.P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 30-33

• PubMed: 24419612 
• DOI: https://doi.org/10.1107/S2053230X13032974
• Primary Citation of Related Structures:  
  4LP9


• PubMed Abstract: 
  

  Endothiapepsin is a typical member of the aspartic proteinase family. The catalytic mechanism of this family is attributed to two conserved catalytic aspartate residues, which coordinate the hydrolysis of a peptide bond. An oligopeptide inhibitor (IC50 = 0.62 µM) based on a reduced-bond transition-state inhibitor of mucorpepsin was co-crystallized with endothiapepsin and the crystal structure of the enzyme-inhibitor complex was determined at 1.35 Å resolution. A total of 12 hydrogen bonds between the inhibitor and the active-site residues were identified. The resulting structure demonstrates a number of novel subsite interactions in the active-site cleft.

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Organizational Affiliation: 

Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF, England.

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: 35.65 kDa 
• Atom Count: 2,853 
• Modelled Residue Count: 337 
• Deposited Residue Count: 337 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro	B [auth I]	7	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001157	B [auth I]	Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.165 
• R-Value Work: 0.123 
• R-Value Observed: 0.125 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.62	α = 90
b = 72.787	β = 108.54
c = 45.113	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
FFT	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
FFT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Guo, J., Cooper, J.B., Wood, S.P.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-20
  Changes: Structure summary