[English] 日本語
Yorodumi
- PDB-1xy8: NMR strcutre of sst1-selective somatostatin (SRIF) analog 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xy8
TitleNMR strcutre of sst1-selective somatostatin (SRIF) analog 1
ComponentsSST1-selective somatosatin analog
KeywordsHORMONE/GROWTH FACTOR / Gamma turn / HORMONE-GROWTH FACTOR COMPLEX
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGrace, C.R.R. / Durrer, L. / Koerber, S.C. / Erchegyi, J. / Reubi, J.C. / Rivier, J.E. / Riek, R.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Somatostatin receptor 1 selective analogues: 4. Three-dimensional consensus structure by NMR
Authors: Grace, C.R.R. / Durrer, L. / Koerber, S.C. / Erchegyi, J. / Reubi, J.C. / Rivier, J.E. / Riek, R.
History
DepositionNov 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SST1-selective somatosatin analog


Theoretical massNumber of molelcules
Total (without water)1,6891
Polymers1,6891
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)10 / 20target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide SST1-selective somatosatin analog / SRIF


Mass: 1689.028 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide synthesised using solid phase approach either manually or on a CS-Biopeptide synthesizer Model CS536

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
1212D NOESY
NMR detailsText: The structure was determined using standard 2D homonuclear techniques

-
Sample preparation

DetailsContents: 2.5 mM of the peptide / Solvent system: DMSO-d6
Sample conditionspH: 7.0 / Pressure: Ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DYANA1.0.6Peter Guntertstructure solution
DYANA1.0.6Peter Guntertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The structures are based on 151 distance restraints, 36 angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 10

+
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