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- PDB-5mng: Cationic trypsin in complex with benzamidine (deuterated sample a... -

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Basic information

Entry
Database: PDB / ID: 5mng
TitleCationic trypsin in complex with benzamidine (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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 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 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_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.auth_comp_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 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 2.2Nov 13, 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)23,8697
Polymers23,3241
Non-polymers5446
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-54 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.486, 58.177, 66.833
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-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.27 Å3/Da / Density % sol: 45.83 %
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: 0.86→43.881 Å / Num. obs: 179771 / % possible obs: 99.8 % / Redundancy: 6.426 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 26.56
Reflection shellResolution: 0.86→0.91 Å / Redundancy: 6.316 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 3.22 / % possible all: 99.4

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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: 0.86→24.672 Å / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 7.79
RfactorNum. reflection% reflectionSelection details
Rfree0.1094 8986 5 %Random selection
Rwork0.0991 ---
obs0.0997 179654 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.86→24.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 30 320 1973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092071
X-RAY DIFFRACTIONf_angle_d1.1682869
X-RAY DIFFRACTIONf_dihedral_angle_d14.441781
X-RAY DIFFRACTIONf_chiral_restr0.1304
X-RAY DIFFRACTIONf_plane_restr0.009399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8599-0.86970.1932890.1885498X-RAY DIFFRACTION97
0.8697-0.87990.18232970.16455658X-RAY DIFFRACTION100
0.8799-0.89060.16092950.14975604X-RAY DIFFRACTION100
0.8906-0.90190.14922970.14175629X-RAY DIFFRACTION100
0.9019-0.91380.14522980.13345664X-RAY DIFFRACTION100
0.9138-0.92630.13042980.12375656X-RAY DIFFRACTION100
0.9263-0.93950.12512970.11375657X-RAY DIFFRACTION100
0.9395-0.95350.10892980.1035660X-RAY DIFFRACTION100
0.9535-0.96840.11022970.09825639X-RAY DIFFRACTION100
0.9684-0.98430.1012990.09015676X-RAY DIFFRACTION100
0.9843-1.00130.0952960.08565623X-RAY DIFFRACTION100
1.0013-1.01950.09462990.08185669X-RAY DIFFRACTION100
1.0195-1.03910.08822990.07785681X-RAY DIFFRACTION100
1.0391-1.06030.09512960.07175629X-RAY DIFFRACTION100
1.0603-1.08340.08053000.06955697X-RAY DIFFRACTION100
1.0834-1.10860.07532980.06755652X-RAY DIFFRACTION100
1.1086-1.13630.07782980.06485694X-RAY DIFFRACTION100
1.1363-1.1670.07262990.06665671X-RAY DIFFRACTION100
1.167-1.20140.0782980.07035670X-RAY DIFFRACTION100
1.2014-1.24010.08493010.07475704X-RAY DIFFRACTION100
1.2401-1.28450.09332990.07895684X-RAY DIFFRACTION100
1.2845-1.33590.09373000.08245693X-RAY DIFFRACTION100
1.3359-1.39670.10483000.08745702X-RAY DIFFRACTION100
1.3967-1.47030.09663010.08545719X-RAY DIFFRACTION100
1.4703-1.56240.09613020.08515737X-RAY DIFFRACTION100
1.5624-1.6830.10243020.09075718X-RAY DIFFRACTION100
1.683-1.85230.10283040.09865772X-RAY DIFFRACTION100
1.8523-2.12030.10883030.10325771X-RAY DIFFRACTION100
2.1203-2.67080.11323090.10995846X-RAY DIFFRACTION100
2.6708-24.6820.14153170.12575995X-RAY DIFFRACTION99

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