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- PDB-5lgo: Trypsin inhibitors for the treatment of pancreatitis - cpd 15 -

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Basic information

Entry
Database: PDB / ID: 5lgo
TitleTrypsin inhibitors for the treatment of pancreatitis - cpd 15
ComponentsCationic trypsin
KeywordsHYDROLASE / S1 protease / Complex / Inhibitor / pancreatitis
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-6VZ / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.12 Å
AuthorsSchiering, N. / D'Arcy, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Trypsin inhibitors for the treatment of pancreatitis.
Authors: Brandl, T. / Simic, O. / Skaanderup, P.R. / Namoto, K. / Berst, F. / Ehrhardt, C. / Schiering, N. / Mueller, I. / Woelcke, J.
History
DepositionJul 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection / Category: atom_site / reflns_shell / Item: _atom_site.occupancy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cationic trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9514
Polymers23,3241
Non-polymers6273
Water5,026279
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-11 kcal/mol
Surface area9060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.232, 55.232, 106.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-6VZ / (2~{S},4~{S})-1-[4-(aminomethyl)-3-methoxy-phenyl]carbonyl-4-[4-(2-cyclopropylethoxy)-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidin-7-yl]-~{N}-methyl-pyrrolidine-2-carboxamide


Mass: 508.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H36N6O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallization Reservoir Solution = 25% PEG3350, 0.2 M LISO4, 100 mM Bis-Tris pH 6.5 Crystallization Protein Solution = 60 mg/ml in 1 mM HCl, 10 mM CaCl2. Complex Formation Method = Soaking ...Details: Crystallization Reservoir Solution = 25% PEG3350, 0.2 M LISO4, 100 mM Bis-Tris pH 6.5 Crystallization Protein Solution = 60 mg/ml in 1 mM HCl, 10 mM CaCl2. Complex Formation Method = Soaking Crystallization Protocol = equal volumes (0.3ul+0.3ul) Crystallization Method = Vapor diffusion - Hanging drop Crystallization Temperature = 298.0 Cryo Protocol = The crystal was directly flash cooled in the nitrogen gas stream at 100 Kelvin. Crystal from cocrystallization soaked in 1 mM cpd 15 (in DMSO) overnight.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.12→47.83 Å / Num. obs: 73334 / % possible obs: 99.9 % / Redundancy: 5.72 % / Biso Wilson estimate: 8.38 Å2 / Rsym value: 0.044 / Net I/σ(I): 21.26

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.12→35.66 Å / Cor.coef. Fo:Fc: 0.9502 / Cor.coef. Fo:Fc free: 0.8638 / SU R Cruickshank DPI: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.037 / SU Rfree Blow DPI: 0.038 / SU Rfree Cruickshank DPI: 0.036
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 3667 5 %RANDOM
Rwork0.1746 ---
obs0.1757 73333 99.88 %-
Displacement parametersBiso mean: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.3627 Å20 Å20 Å2
2--0.3627 Å20 Å2
3----0.7254 Å2
Refine analyzeLuzzati coordinate error obs: 0.112 Å
Refinement stepCycle: 1 / Resolution: 1.12→35.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 42 279 2021
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011797HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.182467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d614SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes277HARMONIC5
X-RAY DIFFRACTIONt_it1797HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.28
X-RAY DIFFRACTIONt_other_torsion14.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2363SEMIHARMONIC4
LS refinement shellResolution: 1.12→1.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1941 266 4.99 %
Rwork0.1873 5062 -
all0.1877 5328 -
obs--99.88 %

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