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- PDB-1v2l: Benzamidine in complex with bovine trypsin variant X(triple.Glu)bT.D1 -

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Basic information

Entry
Database: PDB / ID: 1v2l
TitleBenzamidine in complex with bovine trypsin variant X(triple.Glu)bT.D1
ComponentsTrypsin
KeywordsHYDROLASE / SERINE PROTEASE / SERINE PROTEINASE
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRauh, D. / Klebe, G. / Stubbs, M.T.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Understanding protein-ligand interactions: the price of protein flexibility
Authors: Rauh, D. / Klebe, G. / Stubbs, M.T.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
Authors: Rauh, D. / Klebe, G. / Sturzebecher, J. / Stubbs, M.T.
#2: Journal: Biol.Chem. / Year: 2002
Title: Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
Authors: Rauh, D. / Reyda, S. / Klebe, G. / Stubbs, M.T.
#3: Journal: J.Mol.Biol. / Year: 2003
Title: Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-Induced Structural Plasticity.
Authors: Reyda, S. / Sohn, C. / Klebe, G. / Rall, K. / Ullmann, D. / Jakubke, H.D. / Stubbs, M.T.
#4: Journal: Chembiochem / Year: 2002
Title: pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design.
Authors: Stubbs, M.T. / Reyda, S. / Dullweber, F. / Moller, M. / Klebe, G. / Dorsch, D. / Mederski, W.W. / Wurziger, H.
#5: Journal: J.Med.Chem. / Year: 1998
Title: Structural and functional analyses of benzamidine-based inhibitors in complex with trypsin: implications for the inhibition of factor Xa, tPA, and urokinase.
Authors: Renatus, M. / Bode, W. / Huber, R. / Sturzebecher, J. / Stubbs, M.T.
History
DepositionOct 17, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 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
T: Trypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7575
Polymers23,4041
Non-polymers3524
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.680, 54.680, 136.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Trypsin / Beta-trypsin


Mass: 23404.371 Da / Num. of mol.: 1
Mutation: N97E, L99Y, Y172S, P173S, G174F, Q175I, S190A, S217E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: PANCREAS / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P00760, trypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 126 / 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: 2.36 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulphate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 313K

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 17, 2002 / Details: NI FILTER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→47.35 Å / Num. obs: 36155

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Processing

Software
NameClassification
CrystalCleardata collection
CrystalCleardata reduction
CNSrefinement
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→10 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER /
RfactorNum. reflection
Rfree0.199 -
Rwork0.189 -
obs-28347
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1635 0 20 126 1781

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