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- PDB-8b49: STRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT (m-t... -

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Basic information

Entry
Database: PDB / ID: 8b49
TitleSTRUCTURE OF PORCINE PANCREATIC ELASTASE BOUND TO A FRAGMENT (m-toluoylcarbonyl group) OF A 5-AZAINDOLE 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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-OW9 / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.19 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 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,3355
Polymers28,8451
Non-polymers4904
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-19 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.190, 58.030, 74.580
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, 285 molecules

#2: Chemical ChemComp-OW9 / 1-(3-methylphenyl)carbonylpyrrolo[3,2-c]pyridine-3-carbonitrile


Mass: 261.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H11N3O / 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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 PILATUS3 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: 1.19→30 Å / Num. obs: 70368 / % possible obs: 99.2 % / Redundancy: 12.211 % / Biso Wilson estimate: 18.287 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Χ2: 0.875 / Net I/σ(I): 19.38 / Num. measured all: 859238 / Scaling rejects: 9
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
1.19-1.2211.1391.2212.355985520750260.7881.27996.5
1.22-1.2512.2760.9873.0160519504249300.8631.02997.8
1.25-1.2912.3640.8043.760027493348550.9110.83898.4
1.29-1.3312.6240.6644.5859320473646990.9450.69299.2
1.33-1.3712.2680.5245.6656619464246150.960.54699.4
1.37-1.4212.5620.4087.2255863448444470.9740.42599.2
1.42-1.4712.4520.2999.5753941434643320.9860.31299.7
1.47-1.5312.6950.22612.4252759417341560.9920.23699.6
1.53-1.612.2440.17515.0649072401240080.9930.18299.9
1.6-1.6812.5070.13319.2447741382438170.9960.13899.8
1.68-1.7712.1310.1122.6244230365036460.9970.11599.9
1.77-1.8812.6820.08129.5744311349634940.9980.08599.9
1.88-2.0112.2050.06534.9439726325632550.9990.068100
2.01-2.1712.0480.05639.4136566303630350.9990.059100
2.17-2.3811.9960.04843.8834032283928370.9990.0599.9
2.38-2.6612.6410.04847.4832501257225710.9990.05100
2.66-3.0711.6970.04449.426575227322720.9990.046100
3.07-3.7611.5290.04153.3422344194019380.9990.04399.9
3.76-5.3111.6320.03855.4117878153915370.9990.0499.9
5.31-3010.2770.03851.1392299008980.9990.0499.8

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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: 1QNJ

1qnj


Resolution: 1.19→30 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.084 / SU ML: 0.021 / SU R Cruickshank DPI: 0.0305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1434 3392 4.8 %RANDOM
Rwork0.1181 ---
obs0.1193 66958 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.98 Å2 / Biso mean: 17.824 Å2 / Biso min: 8.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.64 Å2-0 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.19→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 21 281 2121
Biso mean--31.28 33.15 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0121932
X-RAY DIFFRACTIONr_bond_other_d0.0020.0151758
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.6312654
X-RAY DIFFRACTIONr_angle_other_deg1.6321.5714016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81621.91999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16415283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061513
X-RAY DIFFRACTIONr_chiral_restr0.1180.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022387
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02491
X-RAY DIFFRACTIONr_rigid_bond_restr9.71133690
LS refinement shellResolution: 1.19→1.219 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.258 212 -
Rwork0.244 4794 -
obs--96.51 %

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