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- PDB-173d: MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, M... -

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Basic information

Entry
Database: PDB / ID: 173d
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
Components
  • ACTINOMYCIN DDactinomycin
  • DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN / ANTIBIOTIC / ANTITUMOR / ANTICANCER / CHROMOPHORE / DEPSIPEPTIDE / DNA-ANTIBIOTIC COMPLEX
Function / homologyActinomycin D / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
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 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Feb 15, 2012Group: Other
Revision 1.5Dec 12, 2012Group: Other
Revision 1.6Nov 1, 2017Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_struct_assembly.method_details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: ACTINOMYCIN D
D: ACTINOMYCIN D


Theoretical massNumber of molelcules
Total (without water)7,3724
Polymers7,3724
Non-polymers00
Water1,72996
1
B: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
D: ACTINOMYCIN D

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


Theoretical massNumber of molelcules
Total (without water)7,3724
Polymers7,3724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area2990 Å2
ΔGint-15 kcal/mol
Surface area3060 Å2
MethodPISA
2
A: DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')
C: ACTINOMYCIN D

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


Theoretical massNumber of molelcules
Total (without water)7,3724
Polymers7,3724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3110 Å2
ΔGint-11 kcal/mol
Surface area2810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.900, 61.410, 54.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Atom site foot note1: VALINES 19 A AND 25 B OF ACTINOMYCIN D ARE D-VALINES.
Components on special symmetry positions
IDModelComponents
11C-6-

PXZ

21C-6-

PXZ

31D-6-

PXZ

41D-6-

PXZ

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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.: 2 / Source method: obtained synthetically
#2: Protein/peptide ACTINOMYCIN D / Dactinomycin / DACTINOMYCIN / Dactinomycin


Type: PolypeptidePeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (natural) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS ...ACTINOMYCIN D IS A BICYCLIC PEPTIDE, A MEMBER OF THE ACTINOMYCIN FAMILY. HERE, ACTINOMYCIN D IS REPRESENTED BY THE SEQUENCE (SEQRES)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growpH: 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 formulaSol-ID
12.0 mMoligonucleotide1
210 mM1MgCl2
320 mMcacodylate1
42.0 mMspermine tetrachloride1
51.5 mMActinomycin D1
67.5 %(v/v)MPD11
715 %(v/v)1

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Data collection

DiffractionMean temperature: 123 K
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 1016

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.202 -
obs0.202 1016
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms94 322 0 96 512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.037
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_deg5.9
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: 8 Å / σ(F): 2 / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 5.9

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