[English] 日本語
Yorodumi
- PDB-1e81: Endothiapepsin complex with renin inhibitor MERCK-KGAA-EMD61395 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+81
TitleEndothiapepsin complex with renin inhibitor MERCK-KGAA-EMD61395
ComponentsENDOTHIAPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-M91 / Endothiapepsin
Similarity search - Component
Biological speciesENDOTHIA PARASITICA (chestnut blight fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRead, J.A. / Cooper, J.B. / Toldo, L. / Rippmann, F. / Raddatz, P.
CitationJournal: Thesis / Year: 1999
Title: Refinement of Four Endothiapepsin Inhibitor Complexes. Crystallographic Studies of Cytochrome Ch from Methylobacterium Extorquens and Inhibitor Complexes of Aspartic Proteinases.
Authors: Read, J.A.
History
DepositionSep 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2000Provider: 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 1.2Dec 13, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: BASED ON SUBMISSION 4APE
Remark 700 SHEET DETERMINATION METHOD: BASED ON SUBMISSION 4APE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: ENDOTHIAPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4702
Polymers33,8141
Non-polymers6561
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.470, 73.580, 45.340
Angle α, β, γ (deg.)90.00, 110.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ENDOTHIAPEPSIN


Mass: 33813.855 Da / Num. of mol.: 1 / Fragment: RESIDUES 90-419 / Source method: isolated from a natural source
Source: (natural) ENDOTHIA PARASITICA (chestnut blight fungus)
References: UniProt: P11838, mucorpepsin
#2: Chemical ChemComp-M91 / (2S)-1-{[(2R)-1-{[(2S,3S)-1-cyclohexyl-3-hydroxy-4-(2-oxopyridin-1(2H)-yl)butan-2-yl]amino}-3-(methylsulfanyl)-1-oxopropan-2-yl]amino}-1-oxo-3-phenylpropan-2-yl 4-aminopiperidine-1-carboxylate


Type: peptide-like / Mass: 655.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H49N5O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growpH: 5
Details: BATCH METHOD PROTEIN: 10MG/ML, 50 MM AMMONIUM ACETATE PH 5.0, ~2.2 M AMMONIUM SULPHATE, 1% ACETONE. INHIBITOR WAS ADDED IN A 10:1 STOICHIOMETRIC RATIO.

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 20712 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.125 / Net I/σ(I): 4.8
Reflection shellResolution: 2.05→2.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.379 / % possible all: 89.2

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4APE

4ape


Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.234 -5 %
Rwork0.194 --
obs-20712 94.9 %
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 46 148 2583

+
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