8B53 | pdb_00008b53

Structure of porcine pancreatic elastase bound to a fragment of a 4-azaindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8B53/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2022-09-21 Released: 2023-09-20 
• Deposition Author(s): Ferraroni, M., Gerace, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.135 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.112 (DCC) 
• R-Value Observed: 
  0.114 (Depositor) 

Starting Model: experimental

Literature

X-ray structural study of human neutrophil elastase inhibition with a series of azaindoles, azaindazoles and isoxazolones

Gerace, A., Masini, V., Crocetti, L., Giovannoni, M.P., Ferraroni, M.

(2023) J Mol Struct 1274: 134595

• DOI: https://doi.org/10.1016/j.molstruc.2022.134595

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.21 kDa 
• Atom Count: 2,202 
• Modeled Residue Count: 240 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin-like elastase family member 1	A	266	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OVV (Subject of Investigation/LOI)	B [auth A]	3-methylbenzoic acid C8 H8 O2 GPSDUZXPYCFOSQ-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.135 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.112 (DCC) 
• R-Value Observed: 0.114 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.019	α = 90
b = 57.91	β = 90
c = 74.519	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Ferraroni, M., Gerace, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2026-03-04
  Changes: Refinement description