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- PDB-2des: INTERACTIONS BETWEEN MORPHOLINYL ANTHRACYCLINES AND DNA: THE CRYS... -

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Basic information

Entry
Database: PDB / ID: 2des
TitleINTERACTIONS BETWEEN MORPHOLINYL ANTHRACYCLINES AND DNA: THE CRYSTAL STRUCTURE OF A MORPHOLINO DOXORUBICIN BOUND TO D(CGTACG)
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyChem-DMM / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsCirilli, M. / Bachechi, F. / Ughetto, G. / Colonna, F.P. / Capobianco, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Interactions between morpholinyl anthracyclines and DNA. The crystal structure of a morpholino doxorubicin bound to d(CGTACG).
Authors: Cirilli, M. / Bachechi, F. / Ughetto, G. / Colonna, F.P. / Capobianco, M.L.
#1: Journal: Biochemistry / Year: 1987
Title: Interactions Between an Anthracycline Antibiotic and DNA: Molecular Structure of Daunomycin Complexed to d(CpGpTpApCpG) at 1.2-Angstroms Resolution
Authors: Wang, A.-H.J. / Ughetto, G. / Quigley, G.J. / Rich, A.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Structure of 11-Deoxydaunomycin Bound to DNA Containing a Phosphorothioate
Authors: Williams, L.D. / Egli, M. / Ughetto, G. / Van Der Marel, G.A. / Van Boom, J.H. / Quigley, G.J. / Wang, A.H.-J. / Rich, A. / Frederick, C.A.
History
DepositionMar 16, 1993Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,9767
Polymers3,6182
Non-polymers1,3585
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.010, 18.830, 26.750
Angle α, β, γ (deg.)92.60, 100.50, 94.90
Int Tables number1
Space group name H-MP1

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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.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-DMM / 3'-DESAMINO-3'-(2-METHOXY-4-MORPHOLINYL)-DOXORUBICIN


Mass: 643.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H37NO13
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 5.5 / Method: other
Components of the solutions
*PLUS
IDConc.Crystal-IDChemical formula
118 mM1MgCl2
220 %(v/v)1
31
41
51
61
71

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Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 3988
Reflection
*PLUS

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.192 3588
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 95 79 414
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 3588 / Rfactor obs: 0.192 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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