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- PDB-1d21: BINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO ... -

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Basic information

Entry
Database: PDB / ID: 1d21
TitleBINDING OF THE ANTITUMOR DRUG NOGALAMYCIN AND ITS DERIVATIVES TO DNA: STRUCTURAL COMPARISON
ComponentsDNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyNOGALAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsGao, Y.-G. / Liaw, Y.-C. / Robinson, H. / Wang, A.H.-J.
Citation
Journal: Biochemistry / Year: 1990
Title: Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison.
Authors: Gao, Y.G. / Liaw, Y.C. / Robinson, H. / Wang, A.H.
#1: Journal: Biochemistry / Year: 1989
Title: Antitumor Drug Nogalamycin Binds DNA in Both Grooves Simultaneously: Molecular Structure of Nogalamycin-DNA Complex
Authors: Liaw, Y.-C. / Gao, Y.-G. / Robinson, H. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J.
#2: Journal: Nucleic Acids Res. / Year: 1990
Title: NMR Studies on the Binding of Antitumor Drug Nogalamycin to DNA Hexamer d(CGTACG)
Authors: Robinson, H. / Liaw, Y.-C. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J.
History
DepositionAug 8, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model / Derived calculations
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')
B: DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2824
Polymers3,7072
Non-polymers1,5762
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.310, 26.310, 100.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: DNA chain DNA (5'-D(*(5CM)P*GP*TP*(AS)P*(5CM)P*G)-3')


Mass: 1853.336 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NGM / NOGALAMYCIN


Mass: 787.803 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H49NO16 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, temperature 298.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3MGCL211
4NA CACODYLATE11
5WATER12
6PEG 40012
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.5 mMoligonucleotide1drop
28 mM1dropMgCl2
330 mMsodium cacodylate1drop
40.5 mMnogalamycin1drop
52 %(w/v)PEG4001drop
630 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. all: 5276 / Num. obs: 3386 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.208 3386
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 244 112 77 433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.032
X-RAY DIFFRACTIONn_angle_d0.054
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Refinement
*PLUS
σ(F): 2 / Highest resolution: 1.7 Å / Num. reflection obs: 3386 / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.032
X-RAY DIFFRACTIONn_angle_d0.054

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