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- PDB-1pek: STRUCTURE OF THE COMPLEX OF PROTEINASE K WITH A SUBSTRATE-ANALOGU... -

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Basic information

Entry
Database: PDB / ID: 1pek
TitleSTRUCTURE OF THE COMPLEX OF PROTEINASE K WITH A SUBSTRATE-ANALOGUE HEXA-PEPTIDE INHIBITOR AT 2.2 ANGSTROMS RESOLUTION
Components
  • D-DAL-ALA-NH2
  • PEPTIDE PRO-ALA-PRO-PHE
  • PROTEINASE K
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8/S53 domain / : / 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Peptidase S8/S53 domain / Subtilase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesTritirachium album (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsBetzel, C. / Singh, T.P. / Visanji, M. / Peters, K. / Fittkau, S. / Saenger, W. / Wilson, K.S.
Citation
Journal: J.Biol.Chem. / Year: 1993
Title: Structure of the complex of proteinase K with a substrate analogue hexapeptide inhibitor at 2.2-A resolution.
Authors: Betzel, C. / Singh, T.P. / Visanji, M. / Peters, K. / Fittkau, S. / Saenger, W. / Wilson, K.S.
#1: Journal: Eur.J.Biochem. / Year: 1988
Title: Three-Dimensional Structure of Proteinase K at 0.15-Nm Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
History
DepositionJan 19, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEINASE K
C: PEPTIDE PRO-ALA-PRO-PHE
D: D-DAL-ALA-NH2


Theoretical massNumber of molelcules
Total (without water)29,5483
Polymers29,5483
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.280, 68.280, 107.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: ASN E 168 - TYR E 169 OMEGA = 359.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: SER E 170 - PRO E 171 OMEGA = 75.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: PRO C 3 - PHE C 4 OMEGA = 359.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: RESIDUE ALA D 5 IS D-ALANINE.

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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) Tritirachium album (fungus) / References: UniProt: P06873, peptidase K
#2: Protein/peptide PEPTIDE PRO-ALA-PRO-PHE


Mass: 430.496 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE COMPLETE PEPTIDE IS N-AC-PRO-ALA-PRO-PHE-D-ALA-ALA-NH2 AND IS HYDROLYSED AND REPRESENTED AS CHAINS C AND D
#3: Protein/peptide D-DAL-ALA-NH2


Mass: 158.179 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE COMPLETE PEPTIDE IS N-AC-PRO-ALA-PRO-PHE-D-ALA-ALA-NH2 AND IS HYDROLYSED AND REPRESENTED AS CHAINS C AND D
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE HEXAPEPTIDE IS HYDROLYSED BETWEEN PHE C 4 AND D-ALA D 5. BOTH FRAGMENTS REMAIN BOUND TO THE PROTEIN.
Has protein modificationY
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: PRTK_TRIAL SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ALA 85 VAL 85

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl11
21 M11NaNO3
310 mM11CaCl2

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 12725 / % possible obs: 95 % / Num. measured all: 44167 / Rmerge(I) obs: 0.08

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.165 12725 95 %
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 188 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.012
X-RAY DIFFRACTIONp_angle_d0.0630.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.21
X-RAY DIFFRACTIONp_mcangle_it1.761
X-RAY DIFFRACTIONp_scbond_it1.631.3
X-RAY DIFFRACTIONp_scangle_it2.441
X-RAY DIFFRACTIONp_plane_restr0.1210.02
X-RAY DIFFRACTIONp_chiral_restr0.340.12
X-RAY DIFFRACTIONp_singtor_nbd0.2120.5
X-RAY DIFFRACTIONp_multtor_nbd0.3330.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.270.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.11
X-RAY DIFFRACTIONp_staggered_tor19.915
X-RAY DIFFRACTIONp_orthonormal_tor27.120
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection all: 12725 / σ(F): 0 / Rfactor all: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.9 Å2

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