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- PDB-4bcd: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BO... -

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Basic information

Entry
Database: PDB / ID: 4bcd
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-substituted N-acyl-prolylpyrrolidine inhibitor
ComponentsPROLYL ENDOPEPTIDASE
KeywordsHYDROLASE / ALPHA-BETA-HYDROLASE / AMNESIA / PARKINSONS DISEASE / ALZHEIMERS DISEASE / INHIBITOR
Function / homology
Function and homology information


prolyl oligopeptidase / serine-type endopeptidase activity / proteolysis / 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
1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one / Chem-TDV / Prolyl endopeptidase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVanDerVeken, P. / Fulop, V. / Rea, D. / Gerard, M. / VanElzen, R. / Joossens, J. / Cheng, J.D. / Baekelandt, V. / DeMeester, I. / Lambeir, A.M. / Augustyns, K.
CitationJournal: J.Med.Chem. / Year: 2012
Title: P2-Substituted N-Acylprolylpyrrolidine Inhibitors of Prolyl Oligopeptidase: Biochemical Evaluation, Binding Mode Determination, and Assessment in a Cellular Model of Synucleinopathy.
Authors: Van Der Veken, P. / Fulop, V. / Rea, D. / Gerard, M. / Van Elzen, R. / Joossens, J. / Cheng, J.D. / Baekelandt, V. / De Meester, I. / Lambeir, A.M. / Augustyns, K.
History
DepositionOct 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Non-polymer description
Revision 1.2May 29, 2013Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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
A: PROLYL ENDOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,33212
Polymers80,8641
Non-polymers1,46811
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.760, 99.210, 110.950
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 / PE / POST-PROLINE CLEAVING ENZYME


Mass: 80864.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-TDV / 1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 475.558 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H30FN5O2 / Details: P2-substituted N-acyl-prolylpyrrolidine inhibitor
References: 1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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: 2.5 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 8.5
Details: 18-20% METHOXY-POLYETHYLENE GLYCOL (MPEG) 5K, 20 MM CA(OAC)2, 0.1 M TRIS PH 8.5, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9702
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9702 Å / Relative weight: 1
ReflectionResolution: 1.5→56 Å / Num. obs: 120401 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFS

1qfs


Resolution: 1.5→55.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.277 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18581 4892 4.1 %RANDOM
Rwork0.1583 ---
obs0.15943 115509 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.925 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→55.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 100 964 6765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225949
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9638052
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69524.316285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36715972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331525
X-RAY DIFFRACTIONr_chiral_restr0.1110.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214555
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8661.53528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55425696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.57132421
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8924.52356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 361 -
Rwork0.217 8705 -
obs--98.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3487-0.0133-0.21040.031-0.0270.3774-0.02250.02650.042-0.02940.0101-0.004-0.01550.00650.01240.0581-0.0162-0.00370.01440.01360.018534.86949.16266.009
20.11220.01240.03250.2039-0.01280.1719-0.0037-0.01810.00390.03370.0068-0.0007-0.01270.0098-0.00310.02330.00360.00040.0187-0.00280.003543.21640.602101.657
30.16850.0051-0.02270.2496-0.05510.2406-0.025300.0037-0.04340.01950.04280.0075-0.03150.00590.0206-0.0025-0.01110.01440.00630.015225.42138.92876.422
410.77157.733512.74649.06777.708915.6754-0.0568-0.64270.36840.1513-0.38240.238-0.134-0.79720.43930.0217-0.0067-0.00170.0647-0.02150.014139.73737.62787.127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 72
2X-RAY DIFFRACTION2A73 - 427
3X-RAY DIFFRACTION3A428 - 710
4X-RAY DIFFRACTION4A791

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