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- PDB-5eg4: BOVINE TRYPSIN IN COMPLEX WITH CYCLIC INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 5eg4
TitleBOVINE TRYPSIN IN COMPLEX WITH CYCLIC INHIBITOR
ComponentsCationic trypsin
KeywordsHYDROLASE / METAL-BINDING / DIGESTION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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-5N7 / ACETATE ION / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKnoerlein, A. / Wagner, S. / Heine, A. / Steinmetzer, T. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Optimization of Cyclic Plasmin Inhibitors: From Benzamidines to Benzylamines.
Authors: Hinkes, S. / Wuttke, A. / Saupe, S.M. / Ivanova, T. / Wagner, S. / Knorlein, A. / Heine, A. / Klebe, G. / Steinmetzer, T.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)24,3485
Polymers23,3241
Non-polymers1,0244
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-24 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.502, 61.502, 102.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 167 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-5N7 / (13S,16R)-N-(4-carbamimidoylbenzyl)-16-((N-cyclohexylsulfamoyl)amino)-3,9,15-trioxo-2,10,14-triaza-6(1,4)-piperazina-1, 11(1,4)-dibenzenacycloheptadecaphane-13-carboxamide / MI-133


Mass: 829.022 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H56N10O6S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1.7 M (NH4)2SO4, 18 mM CaCl2, 50 mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.32→20 Å / Num. all: 43989 / Num. obs: 43989 / % possible obs: 93.8 % / Redundancy: 4.2 % / Rsym value: 0.049 / Net I/σ(I): 25.6
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AGG

2agg


Resolution: 1.32→19.656 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2203 5.04 %
Rwork0.1798 --
obs0.1818 43753 93.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→19.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 69 163 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071732
X-RAY DIFFRACTIONf_angle_d0.9682361
X-RAY DIFFRACTIONf_dihedral_angle_d12.78654
X-RAY DIFFRACTIONf_chiral_restr0.083260
X-RAY DIFFRACTIONf_plane_restr0.007322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3198-1.34850.25351250.19332718X-RAY DIFFRACTION99
1.3485-1.37980.24331530.18072701X-RAY DIFFRACTION99
1.3798-1.41430.24841320.16762700X-RAY DIFFRACTION99
1.4143-1.45250.21741460.19372708X-RAY DIFFRACTION99
1.4525-1.49530.30881580.24392651X-RAY DIFFRACTION97
1.4953-1.54350.18641460.15282699X-RAY DIFFRACTION99
1.5435-1.59870.18721610.13172716X-RAY DIFFRACTION100
1.5987-1.66260.20281480.1342758X-RAY DIFFRACTION100
1.6626-1.73830.19541570.13712724X-RAY DIFFRACTION100
1.7383-1.82980.19071240.15142783X-RAY DIFFRACTION100
1.8298-1.94440.3589990.30781966X-RAY DIFFRACTION72
1.9444-2.09440.19121290.17272636X-RAY DIFFRACTION94
2.0944-2.30480.30251180.24951918X-RAY DIFFRACTION69
2.3048-2.63770.16831440.16342820X-RAY DIFFRACTION99
2.6377-3.32060.18861570.16922829X-RAY DIFFRACTION100
3.3206-19.65850.19611060.16082223X-RAY DIFFRACTION73

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