2RG3

Covalent complex structure of elastase

• PDB DOI: https://doi.org/10.2210/pdb2RG3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-10-02 Released: 2008-07-01 
• Deposition Author(s): Huang, W., Yamamoto, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.200 

Literature

X-ray snapshot of the mechanism of inactivation of human neutrophil elastase by 1,2,5-thiadiazolidin-3-one 1,1-dioxide derivatives.

Huang, W., Yamamoto, Y., Li, Y., Dou, D., Alliston, K.R., Hanzlik, R.P., Williams, T.D., Groutas, W.C.

(2008) J Med Chem 51: 2003-2008

• PubMed: 18318470 
• DOI: https://doi.org/10.1021/jm700966p
• Primary Citation of Related Structures:  
  2RG3


• PubMed Abstract: 
  

  The mechanism of action of a general class of mechanism-based inhibitors of serine proteases, including human neutrophil elastase (HNE), has been elucidated by determining the X-ray crystal structure of an enzyme-inhibitor complex. The captured intermediate indicates that processing of inhibitor by the enzyme generates an N-sulfonyl imine functionality that is tethered to Ser195, in accordance with the postulated mechanism of action of this class of inhibitors. The identity of the HNE-N-sulfonyl imine species was further corroborated using electrospray ionization mass spectrometry.

---

Organizational Affiliation: 

Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 24.33 kDa 
• Atom Count: 1,823 
• Modelled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte elastase	A	218	Homo sapiens	Mutation(s): 1  Gene Names: ELA2 EC: 3.4.21.37
UniProt & NIH Common Fund Data Resources
Find proteins for P08246 (Homo sapiens) Explore P08246  Go to UniProtKB:  P08246
PHAROS:  P08246 GTEx:  ENSG00000197561
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P08246-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BG1	A	L-PEPTIDE LINKING	C10 H21 N3 O6 S		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.200 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.2	α = 90
b = 73.2	β = 90
c = 70.1	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Huang, W., Yamamoto, Y.

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary