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- PDB-6t5w: Cationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine Deri... -

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Basic information

Entry
Database: PDB / ID: 6t5w
TitleCationic Trypsin in Complex with a D-Phe-Pro-p-aminopyridine Derivative (cocrystallizaton at 291 K)
ComponentsCationic Trypsin
KeywordsHYDROLASE / PROTEASE / SERINE PROTEASE / DIGESTION / METAL ION BINDING
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 / 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-J5K / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsNgo, K. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
Authors: Ngo, K. / Collins-Kautz, C. / Gerstenecker, S. / Wagner, B. / Heine, A. / Klebe, G.
History
DepositionOct 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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: Cationic Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3885
Polymers25,8061
Non-polymers5824
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-24 kcal/mol
Surface area8920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.019, 56.845, 66.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cationic Trypsin


Mass: 25806.197 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 205 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-J5K / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(6-azanylpyridin-3-yl)methyl]pyrrolidine-2-carboxamide / D-Phe-Pro-p-aminopyridine


Mass: 367.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N5O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.97 Å3/Da / Density % sol: 37.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M (NH4)2SO4, 0.1 M imidazole, 0.1% (w/v) sodium azide, 25% (w/v) PEG8000
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.128→43.115 Å / Num. obs: 76852 / % possible obs: 99.5 % / Redundancy: 5 % / Biso Wilson estimate: 11.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Rsym value: 0.052 / Net I/σ(I): 14.55
Reflection shellResolution: 1.13→1.2 Å / Mean I/σ(I) obs: 2.55 / Num. unique obs: 12065 / CC1/2: 0.836 / Rrim(I) all: 0.539 / Rsym value: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MNK

5mnk


Resolution: 1.13→43.11 Å / SU ML: 0.0792 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 11.934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1453 3843 5 %
Rwork0.1278 73009 -
obs0.1286 76852 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.22 Å2
Refinement stepCycle: LAST / Resolution: 1.13→43.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 37 201 1838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531771
X-RAY DIFFRACTIONf_angle_d0.9032425
X-RAY DIFFRACTIONf_chiral_restr0.0853271
X-RAY DIFFRACTIONf_plane_restr0.0062336
X-RAY DIFFRACTIONf_dihedral_angle_d11.4532659
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.18691270.18722420X-RAY DIFFRACTION90.54
1.14-1.160.19161420.16782688X-RAY DIFFRACTION99.96
1.16-1.170.16291420.16322692X-RAY DIFFRACTION99.93
1.17-1.190.20221390.15592655X-RAY DIFFRACTION99.93
1.19-1.210.15921430.14892713X-RAY DIFFRACTION99.83
1.21-1.230.2011410.14092679X-RAY DIFFRACTION99.82
1.23-1.250.14571420.12572689X-RAY DIFFRACTION99.96
1.25-1.270.15361410.12942682X-RAY DIFFRACTION100
1.27-1.290.16561410.12572689X-RAY DIFFRACTION100
1.29-1.320.14421430.11922718X-RAY DIFFRACTION99.97
1.32-1.340.16411410.11632672X-RAY DIFFRACTION100
1.34-1.370.16931420.11262700X-RAY DIFFRACTION99.96
1.37-1.40.13431420.1112704X-RAY DIFFRACTION99.86
1.4-1.440.15141410.10392679X-RAY DIFFRACTION99.96
1.44-1.480.14041430.10532711X-RAY DIFFRACTION99.79
1.48-1.520.12231410.10162682X-RAY DIFFRACTION99.96
1.52-1.570.12611420.09822704X-RAY DIFFRACTION99.93
1.57-1.630.12411440.09572731X-RAY DIFFRACTION99.93
1.63-1.690.11281420.09932702X-RAY DIFFRACTION99.82
1.69-1.770.11711440.09622732X-RAY DIFFRACTION99.97
1.77-1.860.12131430.10632717X-RAY DIFFRACTION99.86
1.86-1.980.14441440.11212727X-RAY DIFFRACTION99.48
1.98-2.130.1291430.11462728X-RAY DIFFRACTION99.48
2.13-2.350.14621450.12242742X-RAY DIFFRACTION99.69
2.35-2.690.14951450.13242767X-RAY DIFFRACTION99.73
2.69-3.380.15361470.1472784X-RAY DIFFRACTION99.29
3.38-43.110.15241530.15542902X-RAY DIFFRACTION99.12

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