[English] 日本語
Yorodumi
- PDB-4y5k: Endothiapepsin in complex with fragment 274 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y5k
TitleEndothiapepsin in complex with fragment 274
ComponentsEndothiapepsin
KeywordsHYDROLASE / fragment screening / aspartic protease / inhibition
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
(1S)-2-amino-1-(4-fluorophenyl)ethanol / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 Å
AuthorsWang, X. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
BMBF05K13RM1 Germany
Citation
Journal: to be published
Title: Crystallographic Fragment Sreening of an Entire Library
Authors: Wang, X. / Heine, A. / Klebe, G.
#1: Journal: J. Med. Chem. / Year: 2011
Title: A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
Authors: Koester, H. / Craan, T. / Brass, S. / Herhaus, C. / Zentgraf, M. / Neumann, L. / Heine, A. / Klebe, G.
History
DepositionFeb 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endothiapepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3697
Polymers33,8141
Non-polymers5556
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint3 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.306, 73.232, 52.845
Angle α, β, γ (deg.)90.00, 109.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Endothiapepsin / Aspartate protease


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin

-
Non-polymers , 5 types, 287 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-489 / (1S)-2-amino-1-(4-fluorophenyl)ethanol


Mass: 155.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10FNO
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystals obtained by streak-seeding

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.439→42.73 Å / Num. obs: 58762 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.056 / Net I/σ(I): 17
Reflection shellResolution: 1.439→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1492refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.439→29.509 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1498 2934 4.99 %Random selection
Rwork0.1212 ---
obs0.1226 58756 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.439→29.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 35 281 2694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072543
X-RAY DIFFRACTIONf_angle_d1.1743486
X-RAY DIFFRACTIONf_dihedral_angle_d10.95835
X-RAY DIFFRACTIONf_chiral_restr0.07409
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4387-1.46230.23411370.17552599X-RAY DIFFRACTION96
1.4623-1.48750.20011370.162624X-RAY DIFFRACTION100
1.4875-1.51460.19931400.14962676X-RAY DIFFRACTION100
1.5146-1.54370.19011380.12972628X-RAY DIFFRACTION100
1.5437-1.57520.18771410.12632677X-RAY DIFFRACTION100
1.5752-1.60950.15561390.1172638X-RAY DIFFRACTION100
1.6095-1.64690.16881390.11252644X-RAY DIFFRACTION100
1.6469-1.68810.14241410.1092668X-RAY DIFFRACTION100
1.6881-1.73370.16511380.10572650X-RAY DIFFRACTION100
1.7337-1.78470.15181410.10082678X-RAY DIFFRACTION100
1.7847-1.84230.13591400.0982650X-RAY DIFFRACTION100
1.8423-1.90820.14351380.09822657X-RAY DIFFRACTION100
1.9082-1.98460.14571410.10132635X-RAY DIFFRACTION100
1.9846-2.07490.13111400.09842663X-RAY DIFFRACTION100
2.0749-2.18420.12391400.10042666X-RAY DIFFRACTION100
2.1842-2.3210.13431380.10572657X-RAY DIFFRACTION99
2.321-2.50010.12511420.11472679X-RAY DIFFRACTION100
2.5001-2.75160.13841380.11822648X-RAY DIFFRACTION100
2.7516-3.14930.14441420.12432680X-RAY DIFFRACTION100
3.1493-3.96630.16371410.13572677X-RAY DIFFRACTION100
3.9663-29.51470.14891430.15082728X-RAY DIFFRACTION99

+
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