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- PDB-215d: CRYSTAL STRUCTURE OF FOUR MORPHOLINO-DOXORUBICIN ANTICANCER DRUGS... -

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Basic information

Entry
Database: PDB / ID: 215d
TitleCRYSTAL STRUCTURE OF FOUR MORPHOLINO-DOXORUBICIN ANTICANCER DRUGS COMPLEXED WITH D(CGTACG) AND D(CGATCG): IMPLICATIONS IN DRUG-DNA CROSSLINK
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: 1.7 Å
AuthorsGao, Y.-G. / Wang, A.H.-J.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 1995
Title: Crystal structures of four morpholino-doxorubicin anticancer drugs complexed with d(CGTACG) and d(CGATCG): implications in drug-DNA crosslink.
Authors: Gao, Y.G. / Wang, A.H.
History
DepositionJun 22, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Jan 31, 1996Provider: 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 / 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

Downloads & links

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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)2,4532
Polymers1,8091
Non-polymers6441
Water84747
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)4,9064
Polymers3,6182
Non-polymers1,2872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)28.122, 28.122, 53.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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-DMM / 3'-DESAMINO-3'-(2-METHOXY-4-MORPHOLINYL)-DOXORUBICIN


Mass: 643.635 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37NO13
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3BACL211
4NA CACODYLATE11
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 mMDNA hexamer1dropsingle strand
24 mM1dropBaCl2
330 mMsodium cacodylate1drop
42.5 mMspermine1drop
51.2 mMdrug1drop
65 %(v/v)MPD1drop
740 %1reservoir30ml

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. all: 1635 / Observed criterion σ(F): 2

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.189 1635
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 46 47 213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.021
X-RAY DIFFRACTIONn_angle_d
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
Highest resolution: 1.7 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: n_bond_d / Dev ideal: 0.021

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