[English] 日本語
Yorodumi
- PDB-1x26: Solution structure of the AA-mismatch DNA complexed with naphthyr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x26
TitleSolution structure of the AA-mismatch DNA complexed with naphthyridine-azaquinolone
Components
  • 5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3'
  • 5'-D(*CP*TP*AP*AP*CP*AP*GP*AP*AP*TP*G)-3'
KeywordsDNA / AA mismatch / drug
Function / homologyChem-NAZ / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsNakatani, K. / Hagihara, S. / Goto, Y. / Kobori, A. / Hagihara, M. / Hayashi, G. / Kyo, M. / Nomura, M. / Mishima, M. / Kojima, C.
CitationJournal: Nat.Chem.Biol. / Year: 2005
Title: Small-molecule ligand induces nucleotide flipping in (CAG)n trinucleotide repeats
Authors: Nakatani, K. / Hagihara, S. / Goto, Y. / Kobori, A. / Hagihara, M. / Hayashi, G. / Kyo, M. / Nomura, M. / Mishima, M. / Kojima, C.
History
DepositionApr 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: 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 ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,6334
Polymers6,7142
Non-polymers9192
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 3366.237 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*AP*TP*TP*CP*AP*GP*TP*TP*AP*G)-3'


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-NAZ / N~3~-{3-[(7-METHYL-1,8-NAPHTHYRIDIN-2-YL)AMINO]-3-OXOPROPYL}-N~1~-[(7-OXO-7,8-DIHYDRO-1,8-NAPHTHYRIDIN-2-YL)METHYL]-BET A-ALANINAMIDE / NAPHTYRIDINE-AZAQUINOLONE


Mass: 459.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N7O3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
2322D TOCSY
2422D NOESY
151DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

-
Sample preparation

DetailsContents: 50mM phosphate buffer NA, 100mM NaCl, 0.1mM EDTA / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11506.5ambient 293 K
21506.5ambient 303 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX8002

-
Processing

NMR software
NameVersionDeveloperClassification
MARDIGRAS3Liu, H.refinement
CNS1.1Brunger, A.T.structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 30

+
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