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- PDB-3e16: X-ray structure of human prostasin in complex with Benzoxazole wa... -

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Basic information

Entry
Database: PDB / ID: 3.0E+16
TitleX-ray structure of human prostasin in complex with Benzoxazole warhead peptidomimic, lysine in P3
ComponentsProstasin
KeywordsHYDROLASE / PROSTASIN / HCAP-1 / Channel Activating Protease / inhibitor / ENac / Benzoxazole / Cell membrane / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Transmembrane / Zymogen
Function / homology
Function and homology information


Formation of the cornified envelope / positive regulation of sodium ion transport / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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-B4C / Prostasin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsSpraggon, G. / Hornsby, M. / Shipway, A. / Harris, J.L. / Lesley, S.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Discovery of inhibitors of the channel-activating protease prostasin (CAP1/PRSS8) utilizing structure-based design.
Authors: Tully, D.C. / Vidal, A. / Chatterjee, A.K. / Williams, J.A. / Roberts, M.J. / Petrassi, H.M. / Spraggon, G. / Bursulaya, B. / Pacoma, R. / Shipway, A. / Schumacher, A.M. / Danahay, H. / Harris, J.L.
History
DepositionAug 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Prostasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4514
Polymers29,6081
Non-polymers8433
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.253, 55.009, 82.799
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prostasin / Serine protease 8 / Prostasin light chain / Prostasin heavy chain


Mass: 29608.002 Da / Num. of mol.: 1 / Fragment: UNP residues 45-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q16651, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-B4C / benzyl [(1S)-5-amino-1-{[(1S)-1-({(1S)-5-amino-1-[(S)-1,3-benzoxazol-2-yl(hydroxy)methyl]pentyl}carbamoyl)-3-phenylpropyl]carbamoyl}pentyl]carbamate


Mass: 672.814 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N6O6
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% PEG-6000 buffered with 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 30043 / Num. obs: 30043 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.601 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→45.819 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1342 5.09 %RANDOM
Rwork0.1852 ---
all0.1875 26355 --
obs0.1875 26355 92 %-
Displacement parametersBiso mean: -0.9314 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.9821 Å2-
3----8.7038 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 59 200 2138

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