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- PDB-3eq9: Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type i... -

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Basic information

Entry
Database: PDB / ID: 3eq9
TitleProlyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type inhibitors
ComponentsProlyl endopeptidase
KeywordsHydrolase/Hydrolase inhibitor / protease-inhibitor complex / Hydrolase / Protease / Serine protease / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / serine-type endopeptidase activity / proteolysis / cytosol / cytoplasm
Similarity search - Function
Prolyl oligopeptidase, N-terminal domain / : / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller ...Prolyl oligopeptidase, N-terminal domain / : / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 7 Propeller / Methylamine Dehydrogenase; Chain H / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-X97 / Prolyl endopeptidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.47 Å
AuthorsKanai, K. / Aranyi, P. / Bocskei, Z. / Ferenczy, G. / Harmat, V. / Simon, K. / Naray-Szabo, G. / Hermecz, I.
CitationJournal: J.Med.Chem. / Year: 2008
Title: Prolyl oligopeptidase inhibition by N-acyl-pro-pyrrolidine-type molecules
Authors: Kanai, K. / Aranyi, P. / Bocskei, Z. / Ferenczy, G. / Harmat, V. / Simon, K. / Batori, S. / Naray-Szabo, G. / Hermecz, I.
History
DepositionSep 30, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jan 18, 2012Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3532
Polymers80,8641
Non-polymers4891
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.550, 101.460, 112.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Prolyl endopeptidase / prolyl oligopeptidase / PE / Post-proline cleaving enzyme


Mass: 80864.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Tissue: muscle / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-X97 / 3-{4-oxo-4-[(2S)-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]butyl}-5,5-diphenylimidazolidine-2,4-dione


Mass: 488.578 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H32N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 17% MPEG 5000, 15% glycerol, 20mM calcium acetate, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 1998 / Details: capillary collimator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.47→34.5 Å / Num. all: 28405 / Num. obs: 28405 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 31.94 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4
Reflection shellResolution: 2.47→2.6 Å / Rmerge(I) obs: 0.441 / Num. unique all: 3140 / % possible all: 74.5

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Processing

Software
NameVersionClassification
bioteXdata collection
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1QFS

1qfs


Resolution: 2.47→34.5 Å
Isotropic thermal model: Grouped isotropic B-factors, 2 B-values/residue
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2438 2819 RANDOM
Rwork0.1744 --
obs0.1744 28372 -
all-28372 -
Displacement parametersBiso mean: 27.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.2436 Å / Luzzati sigma a obs: 0.246 Å
Refinement stepCycle: LAST / Resolution: 2.47→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5659 0 36 132 5827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.182
X-RAY DIFFRACTIONx_dihedral_angle_d27.95

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