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- PDB-2xdw: Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Di... -

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Basic information

Entry
Database: PDB / ID: 2xdw
TitleInhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide
Components
  • Prolyl endopeptidase
  • SYNTHETIC PEPTIDE PHQ-PRO-YCP
KeywordsHYDROLASE / ALPHA/BETA-HYDROLASE / AMNESIA / BETA-PROPELLER / 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
: / Prolyl endopeptidase
Similarity search - Component
Biological speciesSus scrofa (pig)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRacys, D.T. / Rea, D. / Fulop, V. / Wills, M.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Inhibition of Prolyl Oligopeptidase with a Synthetic Unnatural Dipeptide
Authors: Racys, D.T. / Rea, D. / Fulop, V. / Wills, M.
History
DepositionMay 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.2Mar 28, 2012Group: Other
Revision 1.3Dec 28, 2016Group: Source and taxonomy / Version format compliance
Revision 1.4Dec 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.0Aug 7, 2024Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_molecule_features / pdbx_poly_seq_scheme / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id ..._atom_site.auth_seq_id / _atom_site_anisotrop.pdbx_auth_seq_id / _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 / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 2.1Nov 6, 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
P: SYNTHETIC PEPTIDE PHQ-PRO-YCP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,23512
Polymers81,2432
Non-polymers99210
Water19,2401068
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.820, 99.510, 110.790
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: Protein/peptide SYNTHETIC PEPTIDE PHQ-PRO-YCP


Type: Peptide-like / Class: Inhibitor / Mass: 378.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: BIRD: PRD_000694
#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.: 1068 / 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 CCD / 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: 1.35→51.2 Å / Num. obs: 168431 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.4
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.1 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QFS

1qfs


Resolution: 1.35→51.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.675 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.1862 6767 4 %RANDOM
Rwork0.16356 ---
obs0.16448 161664 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.35→51.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5726 0 65 1068 6859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225938
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.968034
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39824.316285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15615972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2241525
X-RAY DIFFRACTIONr_chiral_restr0.1180.2844
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214538
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_it0.8651.53528
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56625696
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61432410
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9374.52338
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: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 475 -
Rwork0.307 12033 -
obs--98.97 %
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)
10.4688-0.0724-0.29630.030.04360.4539-0.02450.02270.0519-0.02350.007-0.011-0.01310.0090.01740.0505-0.01310.00010.010.00920.019534.67149.49765.875
20.10330.00270.03560.192-0.01950.1259-0.0051-0.01490.00530.03180.00540.0004-0.01130.005-0.00030.0190.0041-0.00040.0079-0.00330.001743.31240.78101.472
30.1674-0.0227-0.02820.2222-0.05340.1985-0.0218-0.0012-0.0005-0.03730.01540.02880.0076-0.02560.00640.0164-0.0029-0.01080.00560.00410.014225.36538.93676.331
410.7411.26594.75240.63731.99636.32970.0031-0.33850.15260.02670.0548-0.02350.08260.1334-0.0580.0164-0.0001-0.00710.0325-0.00910.012541.137.06284.976
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 DIFFRACTION4P791 - 793

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