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- PDB-5mnb: Cationic trypsin in complex with 2-aminopyridine (deuterated samp... -

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Basic information

Entry
Database: PDB / ID: 5mnb
TitleCationic trypsin in complex with 2-aminopyridine (deuterated sample at 295 K)
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 / 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 / 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 / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.939 Å
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
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 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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 1.3Nov 20, 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)23,6525
Polymers23,3241
Non-polymers3274
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-38 kcal/mol
Surface area8850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.989, 58.537, 67.618
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 (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-2AP / 2-AMINOPYRIDINE


Mass: 95.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H7N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.28 %
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, 15.5-16.5% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.7069 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7069 Å / Relative weight: 1
ReflectionResolution: 0.939→42.662 Å / Num. obs: 141985 / % possible obs: 99.7 % / Redundancy: 8.75 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.59
Reflection shellResolution: 0.939→1 Å / Redundancy: 8.58 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 4.29 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1-2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I8H

4i8h


Resolution: 0.939→16.935 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 6.69
RfactorNum. reflection% reflectionSelection details
Rfree0.107 7090 5 %Random selection
Rwork0.0961 ---
obs0.0966 141875 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.939→16.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 18 177 1801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081901
X-RAY DIFFRACTIONf_angle_d1.1352634
X-RAY DIFFRACTIONf_dihedral_angle_d11.741693
X-RAY DIFFRACTIONf_chiral_restr0.1288
X-RAY DIFFRACTIONf_plane_restr0.009358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9394-0.950.18692260.18444295X-RAY DIFFRACTION97
0.95-0.96120.16182350.16264463X-RAY DIFFRACTION100
0.9612-0.97290.152360.15054474X-RAY DIFFRACTION100
0.9729-0.98530.15432320.13354415X-RAY DIFFRACTION99
0.9853-0.99820.12292330.11814438X-RAY DIFFRACTION100
0.9982-1.01190.11272340.11134455X-RAY DIFFRACTION100
1.0119-1.02630.10672350.09824471X-RAY DIFFRACTION100
1.0263-1.04170.10562340.09054472X-RAY DIFFRACTION100
1.0417-1.05790.09312350.08244457X-RAY DIFFRACTION100
1.0579-1.07530.08632350.07724461X-RAY DIFFRACTION100
1.0753-1.09380.08252360.06914478X-RAY DIFFRACTION100
1.0938-1.11370.06472340.06224445X-RAY DIFFRACTION100
1.1137-1.13510.06192350.05624480X-RAY DIFFRACTION100
1.1351-1.15830.06512350.05544446X-RAY DIFFRACTION100
1.1583-1.18350.06752350.05644473X-RAY DIFFRACTION100
1.1835-1.2110.07422360.0584484X-RAY DIFFRACTION100
1.211-1.24130.072350.06084464X-RAY DIFFRACTION100
1.2413-1.27480.07732370.06214502X-RAY DIFFRACTION100
1.2748-1.31230.06792360.06474474X-RAY DIFFRACTION100
1.3123-1.35470.07652360.06634486X-RAY DIFFRACTION100
1.3547-1.4030.07722380.06854513X-RAY DIFFRACTION100
1.403-1.45920.08982350.06834498X-RAY DIFFRACTION100
1.4592-1.52560.08192370.0714501X-RAY DIFFRACTION100
1.5256-1.60590.08422390.07394523X-RAY DIFFRACTION100
1.6059-1.70650.08132370.07874528X-RAY DIFFRACTION100
1.7065-1.83810.09452400.08634553X-RAY DIFFRACTION100
1.8381-2.02280.1032400.08864560X-RAY DIFFRACTION100
2.0228-2.31480.10012410.09374570X-RAY DIFFRACTION100
2.3148-2.9140.14082430.12234635X-RAY DIFFRACTION100
2.914-16.93740.14462500.13474771X-RAY DIFFRACTION99

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