5A8X

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

• PDB DOI: https://doi.org/10.2210/pdb5A8X/pdb

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


• Deposited: 2015-07-17 Released: 2016-08-03 
• Deposition Author(s): vonNussbaum, F., Li, V.M., Meibom, D., Anlauf, S., Bechem, M., Delbeck, M., Gerisch, M., Harrenga, A., Karthaus, D., Lang, D., Lustig, K., Mittendorf, J., Schaefer, M., Schaefer, S., Schamberger, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.223 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

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: 1,819 
• Modelled Residue Count: 215 
• 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
IUY	E [auth A]	ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate C24 H20 F3 N4 O2 JHIVXCHUXFMPOR-OAQYLSRUSA-O
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
IUY	Binding MOAD:  5A8X	IC50: 6.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.223 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.795	α = 90
b = 73.795	β = 90
c = 70.01	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): vonNussbaum, F., Li, V.M., Meibom, D., Anlauf, S., Bechem, M., Delbeck, M., Gerisch, M., Harrenga, A., Karthaus, D., Lang, D., Lustig, K., Mittendorf, J., Schaefer, M., Schaefer, S., Schamberger, J.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2017-06-28
  Changes: Data collection
• Version 1.2: 2018-12-12
  Changes: Advisory, Data collection, Database references, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary