1L1V | pdb_00001l1v

UNUSUAL ACTD/DNA_TA COMPLEX STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1L1V/pdb
• NAKB: 1L1V

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


• Deposited: 2002-02-20 Released: 2002-03-06 
• Deposition Author(s): Chou, S.-H., Chin, K.-H., Chen, F.-M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 12 
• Conformers Submitted: 6 
• Selection Criteria: structures with the lowest energy 

Literature

Looped Out and Perpendicular: Deformation of Watson-Crick Base Pair Associated with Actinomycin D Binding.

Chou, S.H., Chin, K.H., Chen, F.M.

(2002) Proc Natl Acad Sci U S A 99: 6625

• PubMed: 12011426 
• DOI: https://doi.org/10.1073/pnas.102580399
• Primary Citation Related Structures: 
  1L1V


• PubMed Abstract: 
  

  Many anticancer drugs interact directly with DNA to exert their biological functions. To date, all noncovalent, intercalating drugs interact with DNA exclusively by inserting their chromophores into base steps to form elongated and unwound duplex structures without disrupting the flanking base pairs. By using actinomycin D (ActD)-5'-GXC/CYG-5' complexes as examples, we have found a rather unusual interaction mode for the intercalated drug; the central Watson-Crick X/Y base pairs are looped out and displaced by the ActD chromophore. The looped-out bases are not disordered but interact perpendicularly with the base/chromophore and form specific H bonds with DNA. Such a complex structure provides intriguing insights into how ligand interacts with DNA and enlarges the repertoires for sequence-specific DNA recognition.

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Organizational Affiliation: 
• Institute of Biochemistry, National Chung-Hsing University, Taichung, Taiwan 40227, Republic of China. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.99 kDa 
• Atom Count: 269 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*TP*CP*AP*CP*CP*GP*AP*C)-3'	A	9	N/A

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DVA	B	D-PEPTIDE LINKING	C5 H11 N O2		--
MVA	B	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	B	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	B	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 12 
• Conformers Submitted: 6 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-06 
Deposition Author(s): Chou, S.-H., Chin, K.-H., Chen, F.-M.

Revision History  

• Version 1.0: 2002-03-06
  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: 2012-12-12
  Changes: Other
• Version 2.0: 2023-11-15
  Changes: Advisory, 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: 2024-11-13
  Changes: Structure summary