[English] 日本語
Yorodumi
- PDB-1scy: DETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF SCYLLATOXIN B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1scy
TitleDETERMINATION OF THE THREE-DIMENSIONAL STRUCTURE OF SCYLLATOXIN BY 1H NUCLEAR MAGNETIC RESONANCE
ComponentsSCYLLATOXIN
KeywordsNEUROTOXIN
Function / homologyScorpion short toxins signature. / Scorpion short chain toxin, potassium channel inhibitor / Scorpion short toxin, BmKK2 / Knottin, scorpion toxin-like superfamily / ion channel inhibitor activity / : / toxin activity / extracellular region / Potassium channel toxin alpha-KTx 5.1
Function and homology information
Biological speciesLeiurus quinquestriatus hebraeus (scorpion)
MethodSOLUTION NMR
AuthorsMartins, J.C. / Van De Ven, F.J.M. / Borremans, F.A.M.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Determination of the three-dimensional solution structure of scyllatoxin by 1H nuclear magnetic resonance.
Authors: Martins, J.C. / Van de Ven, F.J. / Borremans, F.A.
#1: Journal: FEBS Lett. / Year: 1990
Title: Solution Conformation of Leiurotoxin I (Scyllatoxin) by 1H Nuclear Magnetic Resonance. Resonance Assignment and Secondary Structure
Authors: Martins, J.C. / Zhang, W. / Tartar, A. / Lazdunski, M. / Borremans, F.A.M.
History
DepositionJun 2, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SCYLLATOXIN


Theoretical massNumber of molelcules
Total (without water)3,4341
Polymers3,4341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Atom site foot note1: CYS 21 - ILE 22 MODEL 2 OMEGA = 149.70 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA 1 - PHE 2 MODEL 6 OMEGA = 211.28 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ASP 24 - LYS 25 MODEL 6 OMEGA = 229.33 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CYS 21 - ILE 22 MODEL 7 OMEGA = 146.08 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: ASP 24 - LYS 25 MODEL 8 OMEGA = 230.57 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
6: GLY 19 - LYS 20 MODEL 10 OMEGA = 219.59 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
7: ASP 24 - LYS 25 MODEL 12 OMEGA = 214.95 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: LYS 20 - CYS 21 MODEL 16 OMEGA = 213.91 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
9: LYS 20 - CYS 21 MODEL 20 OMEGA = 214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
10: ASP 24 - LYS 25 MODEL 21 OMEGA = 213.51 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
11: ALA 1 - PHE 2 MODEL 22 OMEGA = 228.55 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
12: CYS 3 - ASN 4 MODEL 25 OMEGA = 145.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / -
Representative

-
Components

#1: Protein/peptide SCYLLATOXIN


Mass: 3434.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leiurus quinquestriatus hebraeus (scorpion)
Species: Leiurus quinquestriatus / Strain: hebraeus / References: UniProt: P16341

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR software
NameDeveloperClassification
DIANAGUNTERT,BRAUN,WUTHRICHrefinement
AMBERPEARLMAN,CASE,CALDWELL,SIEBEL,SINGH,WEINER,KOLLMANrefinement
NMR ensembleConformers submitted total number: 25

+
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://pdbjlvh1.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