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- PDB-172d: MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, M... -

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Basic information

Entry
Database: PDB / ID: 172d
TitleMULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, MOLECULAR MODELING, AND SPECTROSCOPIC STUDIES OF D(GAAGCTTC)2-ACTINOMYCIN D COMPLEXES AND ITS HOST DNA
ComponentsDNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKamitori, S. / Takusagawa, F.
CitationJournal: J.Am.Chem.Soc. / Year: 1994
Title: Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of d(GAAGCTTC)2-Actinomycin D Complexes and Its Host DNA
Authors: Kamitori, S. / Takusagawa, F.
History
DepositionApr 18, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1May 23, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Other
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
B: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
C: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
D: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)9,7064
Polymers9,7064
Non-polymers00
Water2,522140
1
A: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
B: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
D: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.540, 70.540, 53.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 2426.617 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formula
12.0 mMoligonucleotide1
210 mM1MgCl2
320 mMcacodylate1
42.0 mMspermine tetrachloride1
57.5 %(v/v)MPD1
615 %(v/v)MPD1
71

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Data collection

DiffractionMean temperature: 123 K
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→10 Å / Num. all: 1928 / Num. obs: 1035 / Observed criterion σ(F): 1.5
Reflection
*PLUS
Highest resolution: 3 Å / % possible obs: 93 % / Observed criterion σ(F): 1.5

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3→10 Å / σ(F): 1.5 /
RfactorNum. reflection
Rwork0.212 -
obs0.212 1035
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 644 0 140 784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.039
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg6.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 1.5 / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 6.4

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