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- PDB-6sy3: Cationic Trypsin in Complex with a D-DiPhe-Pro-pyridine derivative -

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Basic information

Entry
Database: PDB / ID: 6sy3
TitleCationic Trypsin in Complex with a D-DiPhe-Pro-pyridine 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-LXW / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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
DepositionSep 27, 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 13, 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)26,3534
Polymers25,8061
Non-polymers5473
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-12 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.485, 56.535, 66.585
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

#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
#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-LXW / (2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)pyrrolidine-2-carboxamide


Mass: 428.526 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.05 %
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, 25-27% (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: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 0.95→43.096 Å / Num. obs: 127390 / % possible obs: 98 % / Redundancy: 4.11 % / Biso Wilson estimate: 8.69 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.043 / Rsym value: 0.038 / Net I/σ(I): 16.04
Reflection shellResolution: 0.95→1.01 Å / Mean I/σ(I) obs: 1.77 / Num. unique obs: 19451 / CC1/2: 0.74 / Rrim(I) all: 0.58 / Rsym value: 0.49

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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: 0.95→33.8 Å / SU ML: 0.0556 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.6436
RfactorNum. reflection% reflection
Rfree0.1338 2224 1.75 %
Rwork0.1235 --
obs0.1237 127390 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.95 Å2
Refinement stepCycle: LAST / Resolution: 0.95→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 37 228 1876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00521878
X-RAY DIFFRACTIONf_angle_d0.9442584
X-RAY DIFFRACTIONf_chiral_restr0.0859283
X-RAY DIFFRACTIONf_plane_restr0.0068367
X-RAY DIFFRACTIONf_dihedral_angle_d16.1631717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.970.21221240.236982X-RAY DIFFRACTION88.38
0.97-0.990.23731350.20027581X-RAY DIFFRACTION95.78
0.99-1.020.16931370.18147698X-RAY DIFFRACTION97.6
1.02-1.040.18131370.15717699X-RAY DIFFRACTION97.49
1.04-1.080.15091380.13337772X-RAY DIFFRACTION98.05
1.08-1.110.14321380.11137796X-RAY DIFFRACTION98.34
1.11-1.150.09911390.09277818X-RAY DIFFRACTION98.81
1.15-1.20.10571390.08987847X-RAY DIFFRACTION98.78
1.2-1.250.1071400.09237839X-RAY DIFFRACTION98.92
1.25-1.320.10151400.09627916X-RAY DIFFRACTION99.35
1.32-1.40.1261410.09967934X-RAY DIFFRACTION99.65
1.4-1.510.11111410.09897944X-RAY DIFFRACTION99.31
1.51-1.660.11991420.10137992X-RAY DIFFRACTION99.6
1.66-1.90.11291420.11218004X-RAY DIFFRACTION99.47
1.9-2.390.11961430.12318025X-RAY DIFFRACTION98.91
2.39-33.80.15871480.14688319X-RAY DIFFRACTION99.12

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