[English] 日本語
Yorodumi
- PDB-1cz6: SOLUTION STRUCTURE OF ANDROCTONIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cz6
TitleSOLUTION STRUCTURE OF ANDROCTONIN
ComponentsPROTEIN (ANDROCTONIN)
KeywordsTOXIN / BETA SHEET
Function / homologydefense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Androctonin
Function and homology information
Biological speciesAndroctonus australis (Sahara scorpion)
MethodSOLUTION NMR
AuthorsMandard, N. / Vovelle, F.
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 1999
Title: Androctonin, a novel antimicrobial peptide from scorpion Androctonus australis: solution structure and molecular dynamics simulations in the presence of a lipid monolayer.
Authors: Mandard, N. / Sy, D. / Maufrais, C. / Bonmatin, J.M. / Bulet, P. / Hetru, C. / Vovelle, F.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Characterization of novel cystein-rich antimicrobial peptides from scorpion blood
Authors: Ehret-Sabatier, L. / Bulet, P.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ANDROCTONIN)


Theoretical massNumber of molelcules
Total (without water)3,0891
Polymers3,0891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Representative

-
Components

#1: Protein/peptide PROTEIN (ANDROCTONIN)


Mass: 3088.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANDROCTONUS / Source: (natural) Androctonus australis (Sahara scorpion) / References: UniProt: P56684
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY

-
Sample preparation

DetailsContents: 3.25 MM
Sample conditionspH: 4 / Pressure: AMBIENT / Temperature: 285 K

-
NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DIANA2.1Guntert, P. et al.structure solution
X-PLOR3.1BRUNGER, A.T. et al.refinement
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH THE LOWEST ENERGY, TARGET FUNCTION
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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