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- PDB-1pfg: Strategy to design inhibitors: Structure of a complex of Proteina... -

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Basic information

Entry
Database: PDB / ID: 1pfg
TitleStrategy to design inhibitors: Structure of a complex of Proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5A resolution
Components
  • N-Ac-PAPFAAAA-NH2
  • Proteinase K
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Proteinase K / octapeptide / inhibitor / complex / hydrolase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSaxena, A.K. / Singh, T.P. / Peters, K. / Fittkau, S. / Betzel, C.
CitationJournal: Protein Sci. / Year: 1996
Title: Strategy to design peptide inhibitors: structure of a complex of proteinase K with a designed octapeptide inhibitor N-Ac-Pro-Ala-Pro-Phe-DAla-Ala-Ala-Ala-NH2 at 2.5 A resolution.
Authors: Saxena, A.K. / Singh, T.P. / Peters, K. / Fittkau, S. / Betzel, C.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.pdbx_database_id_DOI / _citation.title ..._citation.pdbx_database_id_DOI / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteinase K
B: N-Ac-PAPFAAAA-NH2


Theoretical massNumber of molelcules
Total (without water)29,6982
Polymers29,6982
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.000, 68.000, 107.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Proteinase K /


Mass: 28958.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / Tissue: Limber / References: UniProt: P06873, peptidase K
#2: Protein/peptide N-Ac-PAPFAAAA-NH2


Mass: 738.853 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solution phase synthesis
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Tris, 1mM CaCl2, 1M NaHNO3, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 %(w/v)protein1drop
250 mMTris-HCl1drop
31 mM1droppH6.5CaCl2
41 M1reservoirNaNO3

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SEALED TUBE / Type: CONVENTIONAL Cu / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 1995 / Details: Graphite monochromator
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 49646 / Num. obs: 7647 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Rsym value: 0.069
Reflection
*PLUS
Num. measured all: 49646 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
PROLSQrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PEK

1pek


Resolution: 2.5→8 Å / σ(F): 0 / σ(I): 0
Details: The distance between (B PHE 284) and Residue (B ALA 285) is longer than the peptide bond distance as the peptide is hydolysed at this point.
RfactorNum. reflection
Rwork0.167 -
all-7430
obs-7430
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 0 206 2277
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d2.6
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONo_mcbond_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.6
X-RAY DIFFRACTIONp_plane_restr0.031
X-RAY DIFFRACTIONp_chiral_restr0.21

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