5A09

Crystal Structure of human neutrophil elastase in complex with a dihydropyrimidone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5A09/pdb

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


• Deposited: 2015-04-17 Released: 2015-08-19 
• Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, L., Bechem, M., Delbeck, M., Fitzgerald, M.F., Gerisch, M., Gielen-Haertwig, H., Haning, H., Karthaus, D., Lang, D., Lustig, K., Meibom, D., Mittendorf, J., Rosentreter, U., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.239 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

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: 24.73 kDa 
• Atom Count: 1,910 
• Modelled Residue Count: 218 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUTROPHIL ELASTASE	A	218	Homo sapiens	Mutation(s): 0  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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JJD	E [auth A]	2-[(4R)-4-(4-cyanophenyl)-5-ethanoyl-6-methyl-2-oxidanylidene-1-[3-(trifluoromethyl)phenyl]-4H-pyrimidin-3-yl]ethanoic acid C23 H18 F3 N3 O4 RRKQYMJDNSVFCG-OAQYLSRUSA-N
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
JJD	BindingDB:  5A09	IC50: 3.5 (nM) from 1 assay(s)
	Binding MOAD:  5A09	IC50: 3.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.239 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.77	α = 90
b = 72.77	β = 90
c = 69.626	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): vonNussbaum, F., Li, V.M.-J., Allerheiligen, S., Anlauf, S., Baerfacker, L., Bechem, M., Delbeck, M., Fitzgerald, M.F., Gerisch, M., Gielen-Haertwig, H., Haning, H., Karthaus, D., Lang, D., Lustig, K., Meibom, D., Mittendorf, J., Rosentreter, U., Schaefer, M., Schaefer, S., Schamberger, J., Telan, L.A., Tersteegen, A.

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2017-03-22
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2021-04-28
  Changes: Data collection, Structure summary
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description