[English] 日本語
Yorodumi
- PDB-2ky7: NMR Structural Studies on the Covalent DNA Binding of a Pyrrolobe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ky7
TitleNMR Structural Studies on the Covalent DNA Binding of a Pyrrolobenzodiazepine-Naphthalimide Conjugate
Components5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
KeywordsDNA / DNA duplex / Pyrrolobenzodiazepine / PBD-naphthalimide hybrid / DNA-drug complex
Function / homologyChem-HY2 / DNA
Function and homology information
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average and energy minimized, model 1
AuthorsRettig, M. / Langel, W. / Kamal, A. / Weisz, K.
CitationJournal: Org.Biomol.Chem. / Year: 2010
Title: NMR structural studies on the covalent DNA binding of a pyrrolobenzodiazepine-naphthalimide conjugate
Authors: Rettig, M. / Langel, W. / Kamal, A. / Weisz, K.
History
DepositionMay 17, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
B: 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6843
Polymers6,0862
Non-polymers5981
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210.2 Å2
ΔGint-4.7 kcal/mol
Surface area3968.6 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 20000representative conformers of production runs
RepresentativeModel #1closest to the average and energy minimized

-
Components

#1: DNA chain 5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'


Mass: 3043.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-HY2 / 2-{2-[4-(3-{[(11aS)-7-methoxy-5-oxo-2,3,5,10,11,11a-hexahydro-1H-pyrrolo[2,1-c][1,4]benzodiazepin-8-yl]oxy}propyl)piperazin-1-yl]ethyl}-1H-benzo[de]isoquinoline-1,3(2H)-dione


Mass: 597.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39N5O5
Nonpolymer detailsTHE LIGAND HY2 IS REFERRED AS PBD-NAPHTHALIMIDE HYBRID IN THE ARTICLE. THE HY2 IS NEUTRAL BUT ...THE LIGAND HY2 IS REFERRED AS PBD-NAPHTHALIMIDE HYBRID IN THE ARTICLE. THE HY2 IS NEUTRAL BUT BECAME PROTONATED WHEN BOUND TO DNA IN THE BUFFER USED. IN THIS ENTRY, EXTRA HYDROGEN HN16 IS INCLUDED TO THE COMPLEX COORDINATES.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
2222D 1H-1H NOESY
2322D DQF-COSY
2422D 1H-1H TOCSY
2522D-1H-1H ROESY
2622D 31P-1H HETCOR

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 90% H2O/10% D2O90% H2O/10% D2O
21mM DNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3'); 1mM Pyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid; 100mM sodium chloride; 20mM sodium phosphate; 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1 mMDNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-11
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid-21
100 mMsodium chloride-31
20 mMsodium phosphate-41
1 mMDNA (5'-D(*AP*AP*CP*AP*AP*TP*TP*GP*TP*T)-3')-52
1 mMPyrrolo[2,1-c][1,4]benzodiazepine-Naphthalimide Hybrid-62
100 mMsodium chloride-72
20 mMsodium phosphate-82
Sample conditionsIonic strength: 0.28 / pH: 7 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrestrained molecular dynamics
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average and energy minimized
NMR ensembleConformer selection criteria: representative conformers of production runs
Conformers calculated total number: 20000 / Conformers submitted total number: 5 / Representative conformer: 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