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- PDB-8b1y: STRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT OF A... -

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Basic information

Entry
Database: PDB / ID: 8b1y
TitleSTRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT OF A 5-AZAINDAZOLE INHIBITOR
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE / CHYMOTRYPSIN FAMILY / SERINE PROTEASE
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-OTO / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.12 Å
AuthorsFerraroni, M. / Giovannoni, P. / Gerace, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Struct. / Year: 2023
Title: X-ray structural study of human neutrophil elastase inhibition with a series of azaindoles, azaindazoles and isoxazolones
Authors: Gerace, A. / Masini, V. / Crocetti, L. / Giovannoni, M.P. / Ferraroni, M.
History
DepositionSep 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2865
Polymers28,8451
Non-polymers4404
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-19 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.090, 58.050, 74.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Chymotrypsin-like elastase family member 1 / Elastase-1 / PORCINE PANCREATIC ELASTASE


Mass: 28845.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase

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Non-polymers , 5 types, 357 molecules

#2: Chemical ChemComp-OTO / 1-cyclopropylcarbonylpyrazolo[4,3-c]pyridine-3-carbonitrile


Mass: 212.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 31.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: SODIUM SULFATE, SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.12→30 Å / Num. obs: 83858 / % possible obs: 99.2 % / Redundancy: 10.816 % / Biso Wilson estimate: 14.089 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.072 / Χ2: 0.912 / Net I/σ(I): 17.84 / Num. measured all: 907029 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.12-1.156.3280.7592.3837436620559160.7730.82995.3
1.15-1.188.6550.6183.6550606600858470.8980.65797.3
1.18-1.219.8850.5234.7657295586257960.9330.55198.9
1.21-1.2511.3350.4256.2964041568056500.960.44599.5
1.25-1.2911.3110.3587.3562005552254820.9720.37599.3
1.29-1.3411.5150.3028.7161593536253490.9830.31699.8
1.34-1.3911.2540.2510.2358013517351550.9860.26299.7
1.39-1.4411.2560.19312.8455850496749620.990.20299.9
1.44-1.5111.8080.15615.8356454478747810.9930.16499.9
1.51-1.5811.4950.1318.1952660458745810.9950.13699.9
1.58-1.6711.4030.10321.7749670436143560.9960.10799.9
1.67-1.7711.1540.0924.5545900411841150.9970.09499.9
1.77-1.8911.7060.07329.6645667390139010.9980.077100
1.89-2.0411.210.06233.2940793363936390.9980.065100
2.04-2.2411.5680.05537.4638764335333510.9990.05799.9
2.24-2.512.0210.05240.0436773306030590.9990.054100
2.5-2.8912.1790.0542.7833054271527140.9990.052100
2.89-3.5411.7390.04545.0427082230723070.9990.047100
3.54-511.8720.04247.3221774183518340.9990.04499.9
5-3010.9120.04344.5711599106510630.9980.04599.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3HGP

3hgp


Resolution: 1.12→30 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.792 / SU ML: 0.017 / SU R Cruickshank DPI: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1499 4139 4.9 %RANDOM
Rwork0.1268 ---
obs0.1279 79711 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.44 Å2 / Biso mean: 12.634 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0 Å2
2---0.29 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 1.12→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 17 353 2183
Biso mean--18.08 29.36 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0131922
X-RAY DIFFRACTIONr_bond_other_d0.0030.0151754
X-RAY DIFFRACTIONr_angle_refined_deg2.2191.6292644
X-RAY DIFFRACTIONr_angle_other_deg1.6791.574018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15822.25893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3271511
X-RAY DIFFRACTIONr_chiral_restr0.1450.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022371
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02475
X-RAY DIFFRACTIONr_rigid_bond_restr5.49533676
LS refinement shellResolution: 1.12→1.147 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.35 277 -
Rwork0.331 5619 -
obs--95.34 %

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