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 
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 
This is version 2.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
NEUTROPHIL ELASTASE | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P08246 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
JJD Query on 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 Query on NAG | D [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
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 Name | Purpose |
---|---|
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
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 (Full details and data files)
- 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