3HGP

Structure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor FR130180 determined by high resolution crystallography

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.107 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Combined High-Resolution Neutron and X-ray Analysis of Inhibited Elastase Confirms the Active-Site Oxyanion Hole but Rules against a Low-Barrier Hydrogen Bond

Tamada, T., Kinoshita, T., Kurihara, K., Adachi, M., Ohhara, T., Imai, K., Kuroki, R., Tada, T.

(2009) J.Am.Chem.Soc. 131: 11033-11040

  • DOI: 10.1021/ja9028846
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • To help resolve long-standing questions regarding the catalytic activity of the serine proteases, the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. To mimic the tetrahedral transition ...

    To help resolve long-standing questions regarding the catalytic activity of the serine proteases, the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. To mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 A resolution and X-ray data to 1.20 A resolution. Another crystal provided a low-temperature X-ray data set to 0.94 A resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 (chymotrypsin numbering) is 2.60 A in length and that the hydrogen-bonding hydrogen is 0.80-0.96 A from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

    Organizational Affiliation: 

    Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-Shirane, Tokai, Ibaraki 319-1195, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elastase-1
A
240Sus scrofaMutation(s): 0 
Gene Names: CELA1 (ELA1)
EC: 3.4.21.36
Find proteins for P00772 (Sus scrofa)
Go to Gene View: CELA1
Go to UniProtKB:  P00772
Small Molecules
Ligands 3 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
CA
Query on CA
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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FRW
Query on FRW
Download SDF File 
Download CCD File 
A
4-[[(2S)-3-methyl-1-oxo-1-[(2S)-2-[[(3S)-1,1,1-trifluoro-4-methyl-2-oxo-pentan-3-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamoyl]benzoic acid
C24 H30 F3 N3 O6
FGNPKLCZJAUKFU-BZSNNMDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.94 Å
  • R-Value Free: 0.128 
  • R-Value Work: 0.107 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.859α = 90.00
b = 57.049β = 90.00
c = 74.333γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance