Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 26.58 kDa 
• Atom Count: 2290 
• Modelled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

3HGP

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

• DOI: 10.2210/pdb3HGP/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2009-05-14 Released: 2009-07-28 
• Deposition Author(s): Tamada, T., Kinoshita, T., Kuroki, R., Tada, T.

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Experimental Data Snapshot

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

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

• PubMed: 19603802 
• DOI: 10.1021/ja9028846
• Primary Citation of Related Structures:  
  3HGN, 3HGP


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastase-1	A	240	Sus scrofa	Mutation(s): 0  Gene Names: CELA1, ELA1 EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRW	B [auth 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
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 49.859	α = 90
b = 57.049	β = 90
c = 74.333	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-05-14 
• Released Date: 2009-07-28 
Deposition Author(s): Tamada, T., Kinoshita, T., Kuroki, R., Tada, T.

Revision History  

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