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- PDB-1nzm: NMR structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4... -

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Basic information

Entry
Database: PDB / ID: 1nzm
TitleNMR structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 complexed with the telomerase inhibitor RHPS4
Components5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
KeywordsDNA / Quadruplex DNA / telomeres / telomerase inhibition / NMR spectroscopy / molecular dynamics / drug-DNA interaction / TTAGGGT REPEAT
Function / homology: / Chem-LG1 / DNA
Function and homology information
MethodSOLUTION NMR / Restrained molecular dynamics
AuthorsGavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Drug Recognition and Stabilisation of the Parallel-stranded DNA Quadruplex d(TTAGGGT)4 Containing the Human Telomeric Repeat
Authors: Gavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S.
#1: Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2001
Title: Recognition and stabilisation of Quadruplex DNA by a potent new telomerase inhibitor: NMR studies of the 2:1 complex of a pentacyclic Methylacridinium cation with (TTAGGGT)4
Authors: Gavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S.
History
DepositionFeb 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
B: 5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
C: 5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
D: 5'-D(*TP*TP*AP*GP*GP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4478
Polymers8,6744
Non-polymers7734
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 / 100structures with the least restraint violations
RepresentativeModel #10fewest violation

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Components

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


Mass: 2168.445 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-LG1 / 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM


Mass: 347.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17F2N2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
NMR detailsText: This structure was determined using standard 2D NMR techniques

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Sample preparation

DetailsContents: 1.6mM 2:1 RHPS4-d(TTAGGGT)4, 100 mM KCl, 10 mM K2HPO4 buffer, 1 mM EDTA,90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.0 / Pressure: 1 atm / Temperature: 318 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionClassification
ANSIG3.3data analysis
XwinNMR2.7collection
XwinNMR2.7processing
Amber6structure solution
Amber6refinement
RefinementMethod: Restrained molecular dynamics / Software ordinal: 1
Details: The structures are based on a set of 668 NOE restraints, 161 per strand of the quadruplex DNA (TTAGGGT)4 and 24 for both RHPS4 ligands.No hydrogen-bond restraints used.
NMR representativeSelection criteria: fewest violation
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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