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- PDB-4bcb: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND ... -

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Basic information

Entry
Database: PDB / ID: 4bcb
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2- substituted N-acyl-prolylpyrrolidine inhibitor
ComponentsPROLYL ENDOPEPTIDASE
KeywordsHYDROLASE / ALPHA-BETA-HYDROLASE / AMNESIA / BETA-PROPELLER / PARKINSONS DISEASE / ALZHEIMERS DISEASE
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
(5R,6R,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-5-CYCLOHEXYL-6-HYDROXY-3-OXO-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID / Chem-4I4 / Prolyl endopeptidase
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 29, 2013Group: Other
Revision 1.2Dec 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_conn / 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_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)82,25612
Polymers80,8641
Non-polymers1,39211
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.610, 99.360, 110.470
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-4I4 / (5R,6R,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-5-CYCLOHEXYL-6-HYDROXY-3-OXO-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID 6-OXIDE


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 399.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N6O3 / Details: P2- substituted N-acyl-prolylpyrrolidine inhibitor
References: (5R,6R,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-5-CYCLOHEXYL-6-HYDROXY-3-OXO-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID
#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.: 746 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.7→52 Å / Num. obs: 83611 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.7

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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: 1.7→51.31 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.806 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20263 3416 4.1 %RANDOM
Rwork0.16989 ---
obs0.17126 80195 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.798 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2---0.99 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 93 746 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225941
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9618038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4224.316285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69415972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3721525
X-RAY DIFFRACTIONr_chiral_restr0.1060.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214542
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_it0.7931.53528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44725696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.51732413
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9574.52342
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 242 -
Rwork0.316 6055 -
obs--99.79 %
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)
10.617-0.0562-0.42780.07260.0520.7192-0.03590.0470.0709-0.07230.02180.0152-0.0130.00270.01410.1008-0.0114-0.00680.04290.02140.077334.04849.1865.605
20.13780.0270.02650.2719-0.02360.2336-0.0005-0.02780.00790.04760.00480.0055-0.02030.0095-0.00430.07050.00690.00360.0703-0.00860.051643.08340.72101.43
30.25460.0272-0.06240.4025-0.06370.3223-0.0310.00240.01-0.05430.02060.05290.0019-0.04040.01050.0603-0.0013-0.01450.06160.0050.069625.3439.15876.164
4-0.5885-0.03921.320712.54191.15258.5628-0.0298-0.03670.0090.028-0.12480.2225-0.0155-0.16020.15460.0570.00090.01260.07310.01050.06240.47437.08484.686
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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