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- PDB-4an0: PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND ... -

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Basic information

Entry
Database: PDB / ID: 4an0
TitlePROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND INHIBITOR IC-3
ComponentsProlyl endopeptidase
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / AMNESIA / BETA-PROPELLER
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
Chem-2P6 / Prolyl endopeptidase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St-Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. ...Kaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St-Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. / Karttunen, M. / Hokkanen, J. / Bunker, A.
CitationJournal: Biochimie / Year: 2012
Title: Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase.
Authors: Kaszuba, K. / Rog, T. / Danne, R. / Canning, P. / Fulop, V. / Juhasz, T. / Szeltner, Z. / St Pierre, J.F. / Garcia-Horsman, A. / Mannisto, P.T. / Karttunen, M. / Hokkanen, J. / Bunker, A.
History
DepositionMar 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Structure summary
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
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_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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Sep 24, 2025Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_src_gen / struct_ref
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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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)81,5746
Polymers80,8641
Non-polymers7105
Water11,097616
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.300, 99.900, 111.200
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) / Gene: PREP / Organ: BRAIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM105 / References: UniProt: P23687, prolyl oligopeptidase
#2: Chemical ChemComp-2P6 / (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile / KYP-2047, bound form


Mass: 341.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details(2S)-1-[1-(4-PHENYLBUTANOYL)-L-PROLYL] PYRROLIDINE-2-CARBONITRILE (791): COVALENTLY BOUND TO SER554

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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: ESRF / Beamline: BM16 / Wavelength: 1.0074
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Oct 24, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0074 Å / Relative weight: 1
ReflectionResolution: 2.2→58 Å / Num. obs: 40990 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 10
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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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: 2.2→57.74 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.213 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1731 4.2 %RANDOM
Rwork0.16862 ---
obs0.17092 39259 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 49 616 6366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225903
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.9557997
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5495709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96224.316285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7415972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7581525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2843
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214538
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_it0.6051.53524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19725690
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.10632379
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4454.52307
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 105 -
Rwork0.219 2825 -
obs--98.52 %
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)
10.9835-0.1293-0.50810.09590.21981.1141-0.0120.09680.0885-0.07220.01830.033-0.1320.0089-0.00640.1853-0.00490.0090.09940.030.112835.03849.55666.352
20.29580.07360.08360.301-0.06190.4327-0.0212-0.0349-0.00250.0330.01690.0161-0.03740.01130.00440.13840.00280.00740.1348-0.00230.096243.26541.004102.343
30.4270.0398-0.09580.3883-0.09990.6892-0.01710.01350.0091-0.03680.01920.0501-0.0006-0.0598-0.00210.13740.0005-0.0070.11810.00160.092226.0539.59576.713
419.90839.35397.985621.95219.821417.91110.518-0.5276-1.8747-0.1062-0.0784-0.5236-0.1168-0.045-0.43960.1486-0.03940.00310.20330.12330.247441.46437.25885.419
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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