[English] 日本語
Yorodumi
- PDB-2mne: Recognition complex of DNA d(CGACTAGTCG)2 with thiazotropsin anal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mne
TitleRecognition complex of DNA d(CGACTAGTCG)2 with thiazotropsin analogue AIK-18/51
Components5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'
KeywordsDNA / THIAZOTROPSINS / DNA RECOGNITION / ISOTHERMAL TITRATION CALORIMETRY NMR / SELF-ASSEMBLY / MINOR GROOVE BINDER
Function / homologyAIK-18/51 / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsAlniss, H.Y. / Salvia, M.-V. / Sadikov, M. / Golovchenko, I. / Anthony, N.G. / Khalaf, A.I. / Mackay, S.P. / Suckling, C.J. / Parkinson, J.A.
CitationJournal: Chembiochem / Year: 2014
Title: Recognition of the DNA minor groove by thiazotropsin analogues.
Authors: Alniss, H.Y. / Salvia, M.V. / Sadikov, M. / Golovchenko, I. / Anthony, N.G. / Khalaf, A.I. / MacKay, S.P. / Suckling, C.J. / Parkinson, J.A.
History
DepositionApr 3, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3324
Polymers6,0902
Non-polymers1,2412
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1structures with the least restraint violations
RepresentativeModel #1minimized average structure

-
Components

#1: DNA chain 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'


Mass: 3045.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-3B5 / AIK-18/51 / N,N-dimethyl-3-[({2-[({1-methyl-4-[({1-methyl-4-[(pyridin-3-ylcarbonyl)amino]-1H-pyrrol-2-yl}carbonyl)amino]-1H-pyrrol- 2-yl}carbonyl)amino]-5-(propan-2-yl)-1,3-thiazol-4-yl}carbonyl)amino]propan-1-aminium


Mass: 620.746 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H38N9O4S

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-1H COSY

-
Sample preparation

DetailsContents: 2 mM AIK-18/51, 2 mM 5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3', 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMAIK-18/51-11
2 mM5'-D(*CP*GP*AP*CP*TP*AP*GP*TP*CP*G)-3'-21
Sample conditionsIonic strength: 0.05 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
SparkyGoddardpeak picking
SYBYLTriposgeometry optimization
SYBYLTriposstructure solution
SYBYLTriposdata analysis
SYBYLTriposstructure generation
MARDIGRASTriposdata analysis
MARDIGRASTriposstructure solution
MARDIGRASTriposnoe conversion to distances
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmangeometry optimization
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 756 / NOE intraresidue total count: 336 / NOE sequential total count: 123
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1 / Conformers submitted total number: 1

+
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