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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 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / 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
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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


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.
Has protein modificationY

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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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