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- PDB-5mnx: Neutron structure of cationic trypsin in complex with 2-aminopyridine -

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Basic information

Entry
Database: PDB / ID: 5mnx
TitleNeutron structure of cationic trypsin in complex with 2-aminopyridine
ComponentsCationic trypsin
KeywordsHYDROLASE / hydrogen bonding / protonation / protein-ligand interaction
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 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
2-AMINOPYRIDINE / DEUTERATED WATER / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsSchiebel, J. / Schrader, T.E. / Ostermann, A. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.
Authors: Schiebel, J. / Gaspari, R. / Sandner, A. / Ngo, K. / Gerber, H.D. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Aug 23, 2017Group: Atomic model / Category: atom_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 17, 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 2.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)23,4593
Polymers23,3241
Non-polymers1352
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.096, 58.701, 67.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-2AP / 2-AMINOPYRIDINE


Mass: 95.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2
#4: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5, 16% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.675 Å
DetectorType: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.675 Å / Relative weight: 1
ReflectionResolution: 1.42→25 Å / Num. obs: 38142 / % possible obs: 90.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.493
Reflection shellResolution: 1.42→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 2.051 / % possible all: 69.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2429)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 1.42→22.166 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1913 5.02 %Random selection
Rwork0.1656 ---
obs0.1676 38107 90.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0053622
NEUTRON DIFFRACTIONf_angle_d0.986201
NEUTRON DIFFRACTIONf_dihedral_angle_d11.602911
NEUTRON DIFFRACTIONf_chiral_restr0.085256
NEUTRON DIFFRACTIONf_plane_restr0.006791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4201-1.45560.3769970.33831907NEUTRON DIFFRACTION68
1.4556-1.4950.31441380.25272217NEUTRON DIFFRACTION80
1.495-1.5390.26651490.21622377NEUTRON DIFFRACTION85
1.539-1.58860.26521350.20892502NEUTRON DIFFRACTION89
1.5886-1.64540.24871260.21772589NEUTRON DIFFRACTION91
1.6454-1.71120.23331460.17182637NEUTRON DIFFRACTION94
1.7112-1.78910.25191280.16772714NEUTRON DIFFRACTION95
1.7891-1.88340.19481510.15742663NEUTRON DIFFRACTION95
1.8834-2.00130.19861530.1472649NEUTRON DIFFRACTION94
2.0013-2.15570.18451350.1412679NEUTRON DIFFRACTION94
2.1557-2.37240.18671350.14132530NEUTRON DIFFRACTION89
2.3724-2.71520.16211450.13812798NEUTRON DIFFRACTION97
2.7152-3.41880.18171290.15732910NEUTRON DIFFRACTION99
3.4188-22.16830.16551460.14933022NEUTRON DIFFRACTION99

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