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- PDB-5mnq: Cationic trypsin in complex with a derivative of N-amidinopiperidine -

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Basic information

Entry
Database: PDB / ID: 5mnq
TitleCationic trypsin in complex with a derivative of N-amidinopiperidine
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
Chem-J3I / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.337 Å
AuthorsSchiebel, J. / Ngo, K. / 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 1.3Oct 16, 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)24,40110
Polymers23,3241
Non-polymers1,0779
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-62 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.893, 64.076, 69.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 244 molecules

#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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-J3I / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(1-carbamimidoylpiperidin-4-yl)methyl]pyrrolidine-2-carboxamide


Mass: 400.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M ammonium sulfate, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.337→47.089 Å / Num. obs: 60257 / % possible obs: 98.7 % / Redundancy: 4.192 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.16
Reflection shellResolution: 1.337→1.42 Å / Redundancy: 4.088 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.32 / % possible all: 96.9

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Processing

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

4i8h


Resolution: 1.337→45.352 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.04
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 3013 5 %Random selection
Rwork0.1373 ---
obs0.139 60252 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.337→45.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 63 235 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081774
X-RAY DIFFRACTIONf_angle_d1.1982432
X-RAY DIFFRACTIONf_dihedral_angle_d12.465656
X-RAY DIFFRACTIONf_chiral_restr0.101268
X-RAY DIFFRACTIONf_plane_restr0.008318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.337-1.35790.29251220.2262322X-RAY DIFFRACTION90
1.3579-1.38020.18581360.19852580X-RAY DIFFRACTION100
1.3802-1.4040.23911360.18592595X-RAY DIFFRACTION100
1.404-1.42950.24991380.1832624X-RAY DIFFRACTION99
1.4295-1.4570.20441370.15932598X-RAY DIFFRACTION100
1.457-1.48680.19021360.14912577X-RAY DIFFRACTION100
1.4868-1.51910.15681360.14272577X-RAY DIFFRACTION100
1.5191-1.55440.1751370.13542617X-RAY DIFFRACTION100
1.5544-1.59330.17321370.12562601X-RAY DIFFRACTION100
1.5933-1.63640.191370.11882600X-RAY DIFFRACTION100
1.6364-1.68460.17821370.11442607X-RAY DIFFRACTION100
1.6846-1.73890.17131380.11212611X-RAY DIFFRACTION100
1.7389-1.80110.14761380.10972621X-RAY DIFFRACTION99
1.8011-1.87320.17251360.11332591X-RAY DIFFRACTION99
1.8732-1.95850.14851370.11272608X-RAY DIFFRACTION99
1.9585-2.06170.14831380.11532616X-RAY DIFFRACTION99
2.0617-2.19090.14111380.11422615X-RAY DIFFRACTION99
2.1909-2.360.13621370.11842610X-RAY DIFFRACTION99
2.36-2.59750.16371370.12932608X-RAY DIFFRACTION98
2.5975-2.97330.17071380.14982624X-RAY DIFFRACTION98
2.9733-3.74580.16871410.14622675X-RAY DIFFRACTION98
3.7458-45.37830.19081460.15772762X-RAY DIFFRACTION97

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