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- PDB-7z2i: TRYPSIN (BOVINE) COMPLEXED WITH compound 4 -

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Basic information

Entry
Database: PDB / ID: 7z2i
TitleTRYPSIN (BOVINE) COMPLEXED WITH compound 4
ComponentsSerine protease 1
KeywordsHYDROLASE / trypsin / fragment complex / fluorine containing small molecule inhibitor
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-I9O / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsSchiering, N. / Dalvit, C. / Vulpetti, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2022
Title: Efficient Screening of Target-Specific Selected Compounds in Mixtures by 19 F NMR Binding Assay with Predicted 19 F NMR Chemical Shifts.
Authors: Vulpetti, A. / Lingel, A. / Dalvit, C. / Schiering, N. / Oberer, L. / Henry, C. / Lu, Y.
History
DepositionFeb 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9587
Polymers23,3241
Non-polymers6346
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-6 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.552, 58.299, 66.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Serine protease 1 / Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Pretrypsinogen I / ...Anionic trypsin I / Anionic trypsin-I / Beta-trypsin / Cationic trypsin / Pretrypsinogen I / Trypsin I / Trypsin-I


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


Mass: 78.133 Da / Num. of mol.: 4 / 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-I9O / 5-[[3-(trifluoromethyl)phenyl]methyl]-1,4,6,7-tetrahydroimidazo[4,5-c]pyridine


Mass: 281.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14F3N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG3350, 0.2 M LISO4, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.09→33.43 Å / Num. obs: 80517 / % possible obs: 90 % / Redundancy: 5.17 % / Biso Wilson estimate: 10.023 Å2 / Rmerge F obs: 0.049 / Rmerge(I) obs: 0.044 / Rrim(I) all: 0.049 / Net I/σ(I): 21.96 / Num. measured all: 416162
Reflection shellResolution: 1.09→33.43 Å / Redundancy: 2.51 % / Rmerge F obs: 0.015 / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.01 / Num. measured obs: 2943 / Num. possible: 689 / Num. unique obs: 619 / Rrim(I) all: 0.029 / % possible all: 47.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.5.0063refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse structure

Resolution: 1.09→33.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.611 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / 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
Rfree0.15 4026 5 %RANDOM
Rwork0.1348 ---
obs0.1356 76489 89.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 42.39 Å2 / Biso mean: 9.836 Å2 / Biso min: 3.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.09→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 41 409 2079
Biso mean--12.97 21.41 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211852
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9642540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28525.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67815295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.32152
X-RAY DIFFRACTIONr_chiral_restr0.080.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211408
X-RAY DIFFRACTIONr_rigid_bond_restr0.78931852
X-RAY DIFFRACTIONr_sphericity_free2.6353410
X-RAY DIFFRACTIONr_sphericity_bonded2.16731799
LS refinement shellResolution: 1.09→1.118 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 154 -
Rwork0.136 2941 -
all-3095 -
obs--47.24 %

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