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- PDB-1ld5: STRUCTURE OF BPTI MUTANT A16V -

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Basic information

Entry
Database: PDB / ID: 1ld5
TitleSTRUCTURE OF BPTI MUTANT A16V
ComponentsPANCREATIC TRYPSIN INHIBITOR
KeywordsHydrolase Inhibitor / BPTI / Kunitz fold
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsCierpicki, T. / Otlewski, J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: NMR structures of two variants of bovine pancreatic trypsin inhibitor (BPTI) reveal unexpected influence of mutations on protein structure and stability.
Authors: Cierpicki, T. / Otlewski, J.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Substitutions at the P1' position in BPTI strongly affect the association energy with serine proteinases
Authors: Grzesiak, A. / Helland, R. / Smalas, A.O. / Krowarsch, D. / Dadlez, M. / Otlewski, J.
History
DepositionApr 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PANCREATIC TRYPSIN INHIBITOR


Theoretical massNumber of molelcules
Total (without water)6,5661
Polymers6,5661
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 48structures with the lowest energy,target function
RepresentativeModel #1

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Components

#1: Protein PANCREATIC TRYPSIN INHIBITOR


Mass: 6565.597 Da / Num. of mol.: 1 / Mutation: A16V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00974

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
NMR detailsText: Structure was determined based on homonuclear TOCSY/NOESY techniques using automatic assignment in NOAH/DYANA program

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Sample preparation

DetailsContents: 4mM BPTI_A16V / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0 / pH: 3.1 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8Delaglio, F.; Grzesiek, S.; Vuister, G.; Zhu, G.; Pfeifer, J.; Bax, A.processing
Sparky3.95Goddard, T.D.; Kneller, D.G.data analysis
DYANA1.5Guntert, P.; Mumenthaler, C.; Herrmann, T.structure solution
CNS1Brunger, A.T.; Adams, P.D.; Clore, G.M.; DeLano, W.L., Gros,P.; Grosse-Kunstleve, R.W.; Jiang, J.S.; Kuszewski, J.; Nilges, M.; Pannu, N.S.; Read, R.J.; Rice, L.M.; Simonson, T.; Warren, G.L.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the lowest energy,target function
Conformers calculated total number: 48 / Conformers submitted total number: 10

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