[English] 日本語
Yorodumi
- PDB-3eq9: Prolyl oligopeptidase complexed with R-Pro-(decarboxy-Pro)-Type i... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more