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- PDB-6t0p: Cationic Trypsin in Complex with a D-Phe-Pro-2-aminopyridine deri... -

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Basic information

Entry
Database: PDB / ID: 6t0p
TitleCationic Trypsin in Complex with a D-Phe-Pro-2-aminopyridine derivative
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-M6Q / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 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 3, 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 1.2Oct 16, 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)26,4666
Polymers25,8061
Non-polymers6605
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-25 kcal/mol
Surface area9120 Å2
Unit cell
Length a, b, c (Å)54.568, 56.684, 66.647
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, 204 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.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-M6Q / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(2-azanylpyridin-4-yl)methyl]pyrrolidine-2-carboxamide


Mass: 367.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2 Å3/Da / Density % sol: 38.41 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.188→43.179 Å / Num. obs: 66940 / % possible obs: 99.6 % / Redundancy: 5.71 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.058 / Rsym value: 0.053 / Net I/σ(I): 14.98
Reflection shellResolution: 1.19→1.26 Å / Mean I/σ(I) obs: 2.76 / Num. unique obs: 10620 / CC1/2: 0.858 / Rrim(I) all: 0.542 / Rsym value: 0.492

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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: 1.19→39.31 Å / SU ML: 0.0771 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.0348
RfactorNum. reflection% reflection
Rfree0.1375 3346 5 %
Rwork0.1231 --
obs0.1239 66940 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.5 Å2
Refinement stepCycle: LAST / Resolution: 1.19→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 41 199 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591799
X-RAY DIFFRACTIONf_angle_d0.90832462
X-RAY DIFFRACTIONf_chiral_restr0.0844272
X-RAY DIFFRACTIONf_plane_restr0.006336
X-RAY DIFFRACTIONf_dihedral_angle_d13.6944671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.19-1.210.19961320.16922516X-RAY DIFFRACTION95.77
1.21-1.220.16651360.15092591X-RAY DIFFRACTION99.96
1.22-1.240.14131400.1412659X-RAY DIFFRACTION100
1.24-1.260.14651380.13522619X-RAY DIFFRACTION100
1.26-1.280.17731390.13322636X-RAY DIFFRACTION100
1.28-1.310.18391380.13012623X-RAY DIFFRACTION100
1.31-1.330.16681390.12592646X-RAY DIFFRACTION99.96
1.33-1.360.14141380.11752616X-RAY DIFFRACTION99.96
1.36-1.390.13621390.10482637X-RAY DIFFRACTION99.93
1.39-1.420.1351380.10462632X-RAY DIFFRACTION100
1.42-1.460.15171400.10012657X-RAY DIFFRACTION99.96
1.46-1.50.11791390.09442631X-RAY DIFFRACTION99.93
1.5-1.540.13721390.09362645X-RAY DIFFRACTION99.96
1.54-1.590.12171390.09662639X-RAY DIFFRACTION99.96
1.59-1.650.12391390.0962640X-RAY DIFFRACTION99.89
1.65-1.710.12151400.09512668X-RAY DIFFRACTION99.86
1.71-1.790.12581390.09282637X-RAY DIFFRACTION99.78
1.79-1.890.1061400.09872673X-RAY DIFFRACTION99.79
1.89-20.11571400.10272655X-RAY DIFFRACTION99.71
2-2.160.12381410.10682673X-RAY DIFFRACTION99.65
2.16-2.380.11551410.11492688X-RAY DIFFRACTION99.4
2.38-2.720.12931420.12622687X-RAY DIFFRACTION99.44
2.72-3.430.13921420.14222703X-RAY DIFFRACTION98.82
3.43-39.310.1651480.1552820X-RAY DIFFRACTION98.44

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