4LP9

Endothiapepsin complexed with Phe-reduced-Tyr peptide.


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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 F Struct Biol Commun 70: 30-33

  • DOI: 10.1107/S2053230X13032974

  • 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 (IC ...

    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.


    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endothiapepsin
A
330Cryphonectria parasiticaMutation(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
MoleculeChainsSequence LengthOrganismDetails
Ser-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-Pro
I
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001157
Query on PRD_001157
ISer-Leu-Phe-His-Phenylalanyl-reduced-peptide-bond-Tyrosyl-Thr-ProPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.620α = 90.00
b = 72.787β = 108.54
c = 45.113γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
XDSdata reduction
FFTmodel building
GDAdata collection
FFTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-19
    Type: Database references