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- PDB-452d: ACRIDINE BINDING TO DNA -

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Basic information

Entry
Database: PDB / ID: 452d
TitleACRIDINE BINDING TO DNA
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / INTERCALATION / GROOVE BINDING
Function / homologyChem-9AD / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsThorpe, J.H. / Todd, A.K. / Cardin, C.J.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray ...Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution
Authors: Todd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Wakelin, L.P.G. / Cardin, C.J.
History
DepositionFeb 18, 1999Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,5444
Polymers1,8091
Non-polymers7353
Water52229
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,0888
Polymers3,6182
Non-polymers1,4706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.161, 30.161, 39.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Cell settinghexagonal
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-3016-

MPD

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-9AD / 9-AMINO-(N-(2-DIMETHYLAMINO)ETHYL)ACRIDINE-4-CARBOXAMIDE


Mass: 308.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N4O
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→16 Å

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementResolution: 1.6→16 Å
RfactorNum. reflection
Rfree0.2556 872
all0.2017 -
obs0.2017 -
Refinement stepCycle: LAST / Resolution: 1.6→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 188 87 46 321

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