Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 49.28 kDa 
• Atom Count: 3759 
• Modelled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 1

3Q76

Structure of human neutrophil elastase (uncomplexed)

• DOI: 10.2210/pdb3Q76/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-01-04 Released: 2011-05-11 
• Deposition Author(s): Hansen, G., Niefind, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

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

• PubMed: 21549129 
• DOI: 10.1016/j.jmb.2011.04.047
• Primary Citation of Related Structures:  
  3Q76, 3Q77


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil elastase	A, B	218	Homo sapiens	Mutation(s): 0  Gene Names: ELANE, ELA2 EC: 3.4.21.37
Find proteins for P08246 (Homo sapiens) Explore P08246  Go to UniProtKB:  P08246
NIH Common Fund Data Resources
PHAROS:  P08246 GTEx:  ENSG00000197561

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], L [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.214 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.224	α = 90
b = 123.224	β = 90
c = 68.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-04 
• Released Date: 2011-05-11 
Deposition Author(s): Hansen, G., Niefind, K.

Revision History  

• Version 1.0: 2011-05-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary