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- PDB-1l1v: UNUSUAL ACTD/DNA_TA COMPLEX STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1l1v
TitleUNUSUAL ACTD/DNA_TA COMPLEX STRUCTURE
Components
  • 5'-D(*GP*TP*CP*AP*CP*CP*GP*AP*C)-3'
  • ACTINOMYCIN D
KeywordsDNA/ANTIBIOTIC / ACTINOMYCIN D / ACTINOMYCIN / ANTIBIOTIC / CHROMOPHORE / ANTI CANCER / ANTITUMOR / DEPSIPEPTIDE / MISMATCH / DNA-ANTIBIOTIC COMPLEX
Function / homologyActinomycin D / : / DNA
Function and homology information
Biological speciesSTREPTOMYCES ANTIBIOTICUS (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
AuthorsChou, S.-H. / Chin, K.-H. / Chen, F.-M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Looped Out and Perpendicular: Deformation of Watson-Crick Base Pair Associated with Actinomycin D Binding.
Authors: Chou, S.H. / Chin, K.H. / Chen, F.M.
History
DepositionFeb 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: 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 1.4Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / 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_polymer_linkage / 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_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)3,9602
Polymers3,9602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint3 kcal/mol
Surface area2090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)6 / 12structures with the lowest energy
RepresentativeModel #1

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Components

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


Mass: 2700.788 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein/peptide ACTINOMYCIN D / DACTINOMYCIN


Type: Polypeptide / Class: Antibiotic / Mass: 1259.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ACTINOMYCIN D CONSISTS OF TWO PENTAMER RINGS LINKED BY THE CHROMOPHORE (PXZ)
Source: (gene. exp.) STREPTOMYCES ANTIBIOTICUS (bacteria) / References: NOR: NOR00228, Actinomycin D
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: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY

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Sample preparation

DetailsContents: ACTD/DNA
Sample conditionsIonic strength: 3 mM / pH: 6.8 / Pressure: AMBIENT / Temperature: 278 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
DISCOVER 97MSIrefinement
VNMR 97structure solution
FELIX 97structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING, MOLECULAR DYNAMICS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 216 RESTRAINTS, 180 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 30 DIHEDRAL ANGLE RESTRAINTS, 6 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 12 / Conformers submitted total number: 6

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