[English] 日本語
Yorodumi
- PDB-1tfs: NMR AND RESTRAINED MOLECULAR DYNAMICS STUDY OF THE THREE-DIMENSIO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tfs
TitleNMR AND RESTRAINED MOLECULAR DYNAMICS STUDY OF THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF TOXIN FS2, A SPECIFIC BLOCKER OF THE L-TYPE CALCIUM CHANNEL, ISOLATED FROM BLACK MAMBA VENOM
ComponentsTOXIN FS2
KeywordsTOXIN
Function / homology
Function and homology information


calcium channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesDendroaspis polylepis polylepis (black mamba)
MethodSOLUTION NMR
AuthorsAlbrand, J.-P. / Blackledge, M.J. / Pascaud, F. / Hollecker, M. / Marion, D.
CitationJournal: Biochemistry / Year: 1995
Title: NMR and restrained molecular dynamics study of the three-dimensional solution structure of toxin FS2, a specific blocker of the L-type calcium channel, isolated from black mamba venom.
Authors: Albrand, J.P. / Blackledge, M.J. / Pascaud, F. / Hollecker, M. / Marion, D.
History
DepositionJan 26, 1995Processing site: BNL
Revision 1.0Mar 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 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: TOXIN FS2


Theoretical massNumber of molelcules
Total (without water)7,0401
Polymers7,0401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: CIS PROLINE - PRO 47 MODEL 1 / 2: CIS PROLINE - PRO 47 MODEL 2 / 3: CIS PROLINE - PRO 47 MODEL 3 / 4: CIS PROLINE - PRO 47 MODEL 4 / 5: CIS PROLINE - PRO 47 MODEL 5 / 6: CIS PROLINE - PRO 47 MODEL 6 / 7: CIS PROLINE - PRO 47 MODEL 7 / 8: CIS PROLINE - PRO 47 MODEL 8 / 9: CIS PROLINE - PRO 47 MODEL 9 / 10: CIS PROLINE - PRO 47 MODEL 10 / 11: CIS PROLINE - PRO 47 MODEL 11 / 12: CIS PROLINE - PRO 47 MODEL 12 / 13: CIS PROLINE - PRO 47 MODEL 13 / 14: CIS PROLINE - PRO 47 MODEL 14 / 15: CIS PROLINE - PRO 47 MODEL 15 / 16: CIS PROLINE - PRO 47 MODEL 16 / 17: CIS PROLINE - PRO 47 MODEL 17 / 18: CIS PROLINE - PRO 47 MODEL 18 / 19: CIS PROLINE - PRO 47 MODEL 19 / 20: CIS PROLINE - PRO 47 MODEL 20
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

-
Components

#1: Protein TOXIN FS2


Mass: 7040.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis polylepis polylepis (black mamba)
Species: Dendroaspis polylepis / Strain: polylepis / References: UniProt: P01414
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

NMR softwareName: Discover / Developer: BIOSYM / Classification: refinement
NMR ensembleConformers 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