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- PDB-3prk: INHIBITION OF PROTEINASE K BY METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHL... -

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Basic information

Entry
Database: PDB / ID: 3prk
TitleINHIBITION OF PROTEINASE K BY METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE. AN X-RAY STUDY AT 2.2-ANGSTROMS RESOLUTION
Components
  • METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE
  • PROTEINASE K
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / 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
methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone / Proteinase K
Similarity search - Component
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWolf, W.M. / Bajorath, J. / Mueller, A. / Raghunathan, S. / Singh, T.P. / Hinrichs, W. / Saenger, W.
Citation
Journal: J.Biol.Chem. / Year: 1991
Title: Inhibition of proteinase K by methoxysuccinyl-Ala-Ala-Pro-Ala-chloromethyl ketone. An x-ray study at 2.2-A resolution.
Authors: Wolf, W.M. / Bajorath, J. / Muller, A. / Raghunathan, S. / Singh, T.P. / Hinrichs, W. / Saenger, W.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Synchrotron X-Ray Data Collection and Restrained Least-Squares Refinement of the Crystal Structure of Proteinase K at 1.5 Angstroms Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
#2: Journal: FEBS Lett. / Year: 1986
Title: Crystallization of the Bifunctional Proteinase(Slash)Amylase Inhibitor Pki-3 and of its Complex with Proteinase K
Authors: Pal, G.P. / Betzel, C. / Jany, K.-D. / Saenger, W.
#3: Journal: FEBS Lett. / Year: 1986
Title: Active-Site Geometry of Proteinase K. Crystallographic Study of its Complex with a Dipeptide Chloromethyl Ketone Inhibitor
Authors: Betzel, C. / Pal, G.P. / Struck, M. / Jany, K.-D. / Saenger, W.
#4: Journal: Embo J. / Year: 1984
Title: Three-Dimensional Structure of Fungal Proteinase K Reveals Similarity to Bacterial Subtilisin
Authors: Paehler, A. / Banerjee, A. / Dattagupta, J.K. / Fujiwara, T. / Lindner, K. / Pal, G.P. / Suck, D. / Weber, G. / Saenger, W.
#5: Journal: J.Mol.Biol. / Year: 1975
Title: Crystallization of the Fungal Enzyme Proteinase K and Amino Acid Composition
Authors: Dattagupta, J.K. / Fujiwara, T. / Grishin, E.V. / Lindner, K. / Manor, P.C. / Pieniazek, N.J. / Saenger, W. / Suck, D.
History
DepositionAug 7, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 8, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEINASE K
I: METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4483
Polymers29,4082
Non-polymers401
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-16 kcal/mol
Surface area10150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 68.300, 108.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: CIS PROLINE - PRO E 171
Components on special symmetry positions
IDModelComponents
11E-313-

HOH

21E-430-

HOH

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Components

#1: Protein PROTEINASE K /


Mass: 28930.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Engyodontium album (fungus) / Tissue: limber / Gene: PROK / References: UniProt: P06873, peptidase K
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-ALA-CHLOROMETHYL KETONE


Type: Peptide-like / Class: Inhibitor / Mass: 476.952 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: methoxysuccinyl-alanyl-alanyl-prolyl-alanine chloromethyl ketone
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CHLOROMETHYLKETONE GROUP IS COVALENTLY LINKED WITH THE ACTIVE SITE FUNCTIONAL GROUPS NE2 HIS E ...THE CHLOROMETHYLKETONE GROUP IS COVALENTLY LINKED WITH THE ACTIVE SITE FUNCTIONAL GROUPS NE2 HIS E 69 AND OG SER E 224. THE FORMER HAS SUBSTITUTED FOR CHLORINE AND THE LATTER HAS ATTACKED THE CARBON OF THE KETONE GROUP, THEREBY FORMING THE TETRAHEDRAL CARBON ATOM OF THE TRANSITION STATE ANALOG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 %(w/v)enzyme 1drop
250 mMTris-HCl1drop
31 mM1dropCaCl2
40.75 M1reservoirNaNO3
550 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 11864 / Observed criterion σ(F): 1 / Num. measured all: 53620 / Rmerge F obs: 0.098 / Biso Wilson estimate: 14.6 Å2

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.198 / Highest resolution: 2.2 Å
Refinement stepCycle: LAST / Highest resolution: 2.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 1 170 2224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.009
X-RAY DIFFRACTIONt_angle_deg1.824
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. reflection obs: 11864 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d0.017
X-RAY DIFFRACTIONt_plane_restr0.025

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