[English] 日本語
Yorodumi
- PDB-4y3a: Endothiapepsin in complex with fragment 181 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y3a
TitleEndothiapepsin in complex with fragment 181
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
Chem-45O / ACETATE ION / Endothiapepsin
Similarity search - Component
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsEhrmann, F.R. / 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: Ehrmann, F.R. / 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 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name
Revision 1.2Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 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)34,88912
Polymers33,8141
Non-polymers1,07511
Water5,621312
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint0 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.169, 72.992, 52.560
Angle α, β, γ (deg.)90.00, 109.11, 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 , 6 types, 323 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-45O / 6-{[(3R,5S)-3,5-dimethylpiperidin-1-yl]methyl}-N,N-dimethyl-1,3,5-triazine-2,4-diamine


Mass: 264.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H24N6
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1M 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: Apr 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.17→42.68 Å / Num. obs: 102974 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rsym value: 0.032 / Net I/σ(I): 19.9
Reflection shellResolution: 1.17→1.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.3 / % possible all: 72.4

-
Processing

Software
NameVersionClassification
PHENIXdev_1779refinement
XDSdata reduction
PHASERphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PCW

3pcw


Resolution: 1.17→42.68 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 10.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1294 5148 5 %random selection
Rwork0.1109 ---
obs0.1119 102973 94.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.17→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 71 312 2762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062656
X-RAY DIFFRACTIONf_angle_d1.2553650
X-RAY DIFFRACTIONf_dihedral_angle_d10.649895
X-RAY DIFFRACTIONf_chiral_restr0.071425
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1698-1.18310.1671090.13132067X-RAY DIFFRACTION60
1.1831-1.1970.14951190.12672273X-RAY DIFFRACTION66
1.197-1.21160.13741330.12172512X-RAY DIFFRACTION74
1.2116-1.22690.14681400.1222671X-RAY DIFFRACTION79
1.2269-1.24310.14931550.11592950X-RAY DIFFRACTION86
1.2431-1.26010.14551630.11153100X-RAY DIFFRACTION91
1.2601-1.27810.13721760.11213329X-RAY DIFFRACTION98
1.2781-1.29720.11461810.10173442X-RAY DIFFRACTION100
1.2972-1.31740.13821810.09833441X-RAY DIFFRACTION100
1.3174-1.3390.11921780.09423387X-RAY DIFFRACTION100
1.339-1.36210.10761820.09553448X-RAY DIFFRACTION100
1.3621-1.38690.1161790.0943407X-RAY DIFFRACTION100
1.3869-1.41360.1221780.0933382X-RAY DIFFRACTION100
1.4136-1.44240.11691790.08873396X-RAY DIFFRACTION100
1.4424-1.47380.11411820.0873465X-RAY DIFFRACTION100
1.4738-1.50810.1131810.08933444X-RAY DIFFRACTION100
1.5081-1.54580.11251790.08733402X-RAY DIFFRACTION100
1.5458-1.58760.10331810.08743426X-RAY DIFFRACTION100
1.5876-1.63430.11171800.08713420X-RAY DIFFRACTION100
1.6343-1.68710.10431800.08863431X-RAY DIFFRACTION100
1.6871-1.74740.10871810.09193435X-RAY DIFFRACTION100
1.7474-1.81730.1041810.09033428X-RAY DIFFRACTION100
1.8173-1.90010.10411790.09363419X-RAY DIFFRACTION100
1.9001-2.00020.11631810.09333424X-RAY DIFFRACTION100
2.0002-2.12550.10481800.09063423X-RAY DIFFRACTION100
2.1255-2.28960.10861820.09573462X-RAY DIFFRACTION100
2.2896-2.520.12761810.11043447X-RAY DIFFRACTION100
2.52-2.88460.13921810.11713423X-RAY DIFFRACTION100
2.8846-3.6340.12521820.12963460X-RAY DIFFRACTION100
3.634-42.70850.19351840.16243511X-RAY DIFFRACTION100

+
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