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

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Basic information

Entry
Database: PDB / ID: 5mnh
TitleCationic trypsin in complex with benzamidine (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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 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 / struct_site_gen
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_atom_id / _atom_site.label_comp_id / _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 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_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 6, 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)23,6775
Polymers23,3241
Non-polymers3524
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-31 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.901, 58.614, 67.604
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-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.: 181 / 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: 47.25 %
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, 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: 0.7749 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: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.93→42.618 Å / Num. obs: 145727 / % possible obs: 99.5 % / Redundancy: 8.633 % / Rsym value: 0.039 / Net I/σ(I): 28.68
Reflection shellResolution: 0.93→0.99 Å / Redundancy: 8.435 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 4.47 / % possible all: 98.8

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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: 0.93→27.451 Å / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 6.37
RfactorNum. reflection% reflectionSelection details
Rfree0.1012 7284 5 %Random selection
Rwork0.0941 ---
obs0.0945 145638 99.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.93→27.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 20 181 1813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081946
X-RAY DIFFRACTIONf_angle_d1.0892698
X-RAY DIFFRACTIONf_dihedral_angle_d11.841717
X-RAY DIFFRACTIONf_chiral_restr0.097293
X-RAY DIFFRACTIONf_plane_restr0.008368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9303-0.94080.18532340.17284446X-RAY DIFFRACTION98
0.9408-0.95190.15042400.15374564X-RAY DIFFRACTION99
0.9519-0.96350.13752380.14374519X-RAY DIFFRACTION99
0.9635-0.97570.15232400.13314548X-RAY DIFFRACTION100
0.9757-0.98850.13332390.1214545X-RAY DIFFRACTION99
0.9885-1.00210.11292410.11274573X-RAY DIFFRACTION99
1.0021-1.01640.09882410.09844590X-RAY DIFFRACTION100
1.0164-1.03160.10872400.09044559X-RAY DIFFRACTION100
1.0316-1.04770.08772420.08054588X-RAY DIFFRACTION100
1.0477-1.06490.0762420.0734597X-RAY DIFFRACTION100
1.0649-1.08320.07532410.074585X-RAY DIFFRACTION99
1.0832-1.10290.07152410.06424571X-RAY DIFFRACTION99
1.1029-1.12410.0682400.05794562X-RAY DIFFRACTION99
1.1241-1.14710.0682430.05494614X-RAY DIFFRACTION100
1.1471-1.1720.06022400.05414563X-RAY DIFFRACTION100
1.172-1.19930.06542440.05734622X-RAY DIFFRACTION100
1.1993-1.22930.07212410.05944594X-RAY DIFFRACTION100
1.2293-1.26250.05982430.064610X-RAY DIFFRACTION100
1.2625-1.29970.06592440.06254636X-RAY DIFFRACTION100
1.2997-1.34160.07612420.06454588X-RAY DIFFRACTION100
1.3416-1.38960.07882430.06724615X-RAY DIFFRACTION100
1.3896-1.44520.07412430.06774618X-RAY DIFFRACTION99
1.4452-1.5110.0792430.0694622X-RAY DIFFRACTION100
1.511-1.59060.07232460.07144658X-RAY DIFFRACTION100
1.5906-1.69030.07282450.07784667X-RAY DIFFRACTION100
1.6903-1.82080.09392470.0844678X-RAY DIFFRACTION100
1.8208-2.0040.08912460.08854671X-RAY DIFFRACTION100
2.004-2.29380.09622480.09324714X-RAY DIFFRACTION100
2.2938-2.88940.11832490.11994732X-RAY DIFFRACTION99
2.8894-27.46240.15182580.13114905X-RAY DIFFRACTION99

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