173D | pdb_0000173d

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

• PDB DOI: https://doi.org/10.2210/pdb173D/pdb
• NAKB: 173D

• Classification: DNA/ANTIBIOTIC
• Organism(s): Streptomyces antibioticus
• Mutation(s): No 


• Deposited: 1994-04-18 Released: 1994-10-15 
• Deposition Author(s): Kamitori, S., Takusagawa, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

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

Kamitori, S., Takusagawa, F.

(1994) J Am Chem Soc 116: 4154

• DOI: https://doi.org/10.1021/JA00089A002

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.44 kDa 
• Atom Count: 512 
• Modeled Residue Count: 28 
• Deposited Residue Count: 38 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTINOMYCIN D	C, D	11	Streptomyces antibioticus	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3')	A, B	8	N/A

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DVA	C, D	D-PEPTIDE LINKING	C5 H11 N O2		--
MVA	C, D	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C, D	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001	C, D	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.9	α = 90
b = 61.41	β = 90
c = 54.25	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-10-15 
Deposition Author(s): Kamitori, S., Takusagawa, F.

Revision History  

• Version 1.0: 1994-10-15
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2012-02-15
  Changes: Other
• Version 1.5: 2012-12-12
  Changes: Other
• Version 1.6: 2017-11-01
  Changes: Advisory, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 3.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2024-11-20
  Changes: Structure summary