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- PDB-5mnn: Cationic trypsin in complex with N-amidinopiperidine (deuterated ... -

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Basic information

Entry
Database: PDB / ID: 5mnn
TitleCationic trypsin in complex with N-amidinopiperidine (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
piperidine-1-carboximidamide / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.859 Å
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
Funding support1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind
CitationJournal: Nat Commun / Year: 2018
Title: Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.
Authors: Schiebel, J. / Gaspari, R. / Wulsdorf, T. / Ngo, K. / Sohn, C. / Schrader, T.E. / Cavalli, A. / Ostermann, A. / Heine, A. / Klebe, G.
History
DepositionDec 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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)23,8767
Polymers23,3241
Non-polymers5526
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-60 kcal/mol
Surface area8990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.680, 58.222, 66.849
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-MRZ / piperidine-1-carboximidamide


Mass: 127.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13N3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
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, 17.5% (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: 0.859→42.325 Å / Num. obs: 179705 / % possible obs: 99.1 % / Redundancy: 8.538 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 27.35
Reflection shellResolution: 0.859→0.91 Å / Redundancy: 8.438 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 3.56 / % possible all: 98.5

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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: 0.859→39.858 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 7.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1095 8983 5 %Random selection
Rwork0.0997 ---
obs0.1002 179602 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.859→39.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 30 318 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092064
X-RAY DIFFRACTIONf_angle_d1.2142858
X-RAY DIFFRACTIONf_dihedral_angle_d13.101774
X-RAY DIFFRACTIONf_chiral_restr0.101303
X-RAY DIFFRACTIONf_plane_restr0.009384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8595-0.86920.17292880.18815459X-RAY DIFFRACTION96
0.8692-0.87950.14842960.1625624X-RAY DIFFRACTION99
0.8795-0.89020.15332960.14975622X-RAY DIFFRACTION99
0.8902-0.90150.14352960.13875618X-RAY DIFFRACTION99
0.9015-0.91330.13722980.12985662X-RAY DIFFRACTION99
0.9133-0.92580.11632970.12215640X-RAY DIFFRACTION99
0.9258-0.93910.13112970.11425644X-RAY DIFFRACTION99
0.9391-0.95310.12882970.10665651X-RAY DIFFRACTION100
0.9531-0.9680.10782970.10075643X-RAY DIFFRACTION99
0.968-0.98390.0972980.09075657X-RAY DIFFRACTION99
0.9839-1.00080.08742960.08545629X-RAY DIFFRACTION99
1.0008-1.0190.09763000.08235681X-RAY DIFFRACTION99
1.019-1.03860.08532960.07575628X-RAY DIFFRACTION99
1.0386-1.05980.08272990.07085682X-RAY DIFFRACTION99
1.0598-1.08290.07912980.06865650X-RAY DIFFRACTION99
1.0829-1.10810.07642980.0655670X-RAY DIFFRACTION99
1.1081-1.13580.07072990.06585675X-RAY DIFFRACTION99
1.1358-1.16650.07473000.0645700X-RAY DIFFRACTION100
1.1665-1.20080.07792980.06955656X-RAY DIFFRACTION100
1.2008-1.23960.08743020.07365736X-RAY DIFFRACTION100
1.2396-1.28390.07852970.07785661X-RAY DIFFRACTION99
1.2839-1.33530.0983000.08245706X-RAY DIFFRACTION99
1.3353-1.39610.09313010.08595706X-RAY DIFFRACTION99
1.3961-1.46970.0932990.0855700X-RAY DIFFRACTION99
1.4697-1.56180.09493020.08575743X-RAY DIFFRACTION99
1.5618-1.68230.0993030.09335742X-RAY DIFFRACTION100
1.6823-1.85160.10653040.10215789X-RAY DIFFRACTION100
1.8516-2.11960.11123050.10415806X-RAY DIFFRACTION100
2.1196-2.67030.1373070.11265822X-RAY DIFFRACTION99
2.6703-39.90090.1373190.12746017X-RAY DIFFRACTION99

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