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- PDB-5mn1: Cationic trypsin in complex with 2-aminopyridine (deuterated samp... -

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Basic information

Entry
Database: PDB / ID: 5mn1
TitleCationic trypsin in complex with 2-aminopyridine (deuterated sample at 100 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: 0.79 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 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Author supporting evidence / Data collection / Refinement description
Category: diffrn_source / pdbx_audit_support / refine_hist
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _refine_hist.d_res_high
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 1.3Oct 23, 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)23,8447
Polymers23,3241
Non-polymers5196
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-56 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.692, 58.269, 66.936
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.: 4 / 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.: 384 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
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, 17% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 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: 0.79→42.35 Å / Num. obs: 226625 / % possible obs: 96.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.1
Reflection shellResolution: 0.79→0.84 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3

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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: 0.79→27.346 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 8.44
RfactorNum. reflection% reflectionSelection details
Rfree0.1093 11326 5 %Random selection
Rwork0.0983 ---
obs0.0988 226534 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.79→27.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 28 384 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092153
X-RAY DIFFRACTIONf_angle_d1.1882988
X-RAY DIFFRACTIONf_dihedral_angle_d12.888812
X-RAY DIFFRACTIONf_chiral_restr0.1314
X-RAY DIFFRACTIONf_plane_restr0.009409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.7885-0.79740.19933410.20786482X-RAY DIFFRACTION88
0.7974-0.80680.173670.17916965X-RAY DIFFRACTION94
0.8068-0.81670.18363670.16976975X-RAY DIFFRACTION95
0.8167-0.8270.17153650.16476933X-RAY DIFFRACTION95
0.827-0.83790.16333700.15337019X-RAY DIFFRACTION95
0.8379-0.84940.14663670.14476983X-RAY DIFFRACTION95
0.8494-0.86150.15993650.14226938X-RAY DIFFRACTION94
0.8615-0.87440.14323690.1297002X-RAY DIFFRACTION95
0.8744-0.8880.12283720.11637058X-RAY DIFFRACTION96
0.888-0.90260.12743740.1067104X-RAY DIFFRACTION96
0.9026-0.91810.1163750.10077129X-RAY DIFFRACTION96
0.9181-0.93480.1053730.09517080X-RAY DIFFRACTION96
0.9348-0.95280.0993760.08897160X-RAY DIFFRACTION97
0.9528-0.97230.09683770.08257147X-RAY DIFFRACTION97
0.9723-0.99340.08613750.07787133X-RAY DIFFRACTION97
0.9934-1.01650.08593740.0767102X-RAY DIFFRACTION96
1.0165-1.04190.07753780.07327178X-RAY DIFFRACTION97
1.0419-1.07010.08193780.06827186X-RAY DIFFRACTION98
1.0701-1.10160.07283820.06717259X-RAY DIFFRACTION98
1.1016-1.13720.07473840.06577295X-RAY DIFFRACTION98
1.1372-1.17780.07783840.06867278X-RAY DIFFRACTION98
1.1778-1.2250.08613850.07327322X-RAY DIFFRACTION98
1.225-1.28070.07943860.07817325X-RAY DIFFRACTION99
1.2807-1.34820.08873850.08447316X-RAY DIFFRACTION98
1.3482-1.43270.09333820.08717282X-RAY DIFFRACTION98
1.4327-1.54330.09363910.08647426X-RAY DIFFRACTION99
1.5433-1.69860.10013920.09457450X-RAY DIFFRACTION99
1.6986-1.94430.11353930.10117492X-RAY DIFFRACTION99
1.9443-2.44940.12173960.10217521X-RAY DIFFRACTION99
2.4494-27.36240.1334030.127668X-RAY DIFFRACTION97

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