3Q76

Structure of human neutrophil elastase (uncomplexed)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.861 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


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

Literature

Unexpected active-site flexibility in the structure of human neutrophil elastase in complex with a new dihydropyrimidone inhibitor.

Hansen, G., Gielen-Haertwig, H., Reinemer, P., Schomburg, D., Harrenga, A., Niefind, K.

(2011) J.Mol.Biol. 409: 681-691

  • DOI: 10.1016/j.jmb.2011.04.047
  • Primary Citation of Related Structures:  
  • Also Cited By: 6F5M

  • PubMed Abstract: 

    • Human neutrophil elastase (HNE), a trypsin-type serine protease, is of pivotal importance in the onset and progression of chronic obstructive pulmonary disease (COPD). COPD encompasses a group of slowly progressive respiratory disorders and is a majo ...

    Human neutrophil elastase (HNE), a trypsin-type serine protease, is of pivotal importance in the onset and progression of chronic obstructive pulmonary disease (COPD). COPD encompasses a group of slowly progressive respiratory disorders and is a major medical problem and the fifth leading cause of death worldwide. HNE is a major target for the development of compounds that inhibit the progression of long-term lung function decline in COPD patients. Here, we present the three-dimensional structure of a potent dihydropyrimidone inhibitor (DHPI) non-covalently bound to HNE at a resolution of 2.0 Å. The inhibitor binds to the active site in a unique orientation addressing S1 and S2 subsites of the protease. To facilitate further analysis of this binding mode, we determined the structure of the uncomplexed enzyme at a resolution of 1.86 Å. Detailed comparisons of the HNE:DHPI complex with the uncomplexed HNE structure and published structures of other elastase:inhibitor complexes revealed that binding of DHPI leads to large conformational changes in residues located in the S2 subsite. The rearrangement of residues Asp95-Leu99B creates a deep, well-defined cavity, which is filled by the P2 moiety of the inhibitor molecule to almost perfect shape complementarity. The shape of the S2 subsite in complex with DHPI clearly differs from all other observed HNE structures. The observed structural flexibility of the S2 subsite is a key feature for the understanding of the binding mode of DHPIs in general and the development of new HNE selective inhibitors.

    Organizational Affiliation: 

    Institute of Biochemistry, Department of Chemistry, University of Cologne, Zülpicher Str. 47, D-50674 Cologne, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil elastase
A, B
218Homo sapiensMutation(s): 0 
Gene Names: ELANE (ELA2)
EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens)
Go to Gene View: ELANE
Go to UniProtKB:  P08246
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FUC
Query on FUC
Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.861 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 123.224α = 90.00
b = 123.224β = 90.00
c = 68.822γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
MAR345dtbdata collection
REFMACrefinement
PHENIXrefinement
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance