1DSD | pdb_00001dsd

NMR STUDY OF DNA (5'-D(*GP*AP*TP*GP*CP*TP*TP*C)-3') T:T MISMATCHED DUPLEX COMPLEXED WITH ACTINOMYCIN D, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1DSD/pdb
• NAKB: 1DSD

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


• Deposited: 1996-08-10 Released: 1996-12-07 
• Deposition Author(s): Lian, C., Robinson, H., Wang, A.H.-J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 

Literature

Structure of Actinomycin D Bound with (Gaagcttc)2 and (Gatgcttc)2 and its Binding to the (Cag)N:(Ctg)N Triplet Sequence by NMR Analysis

Lian, C., Robinson, H., Wang, A.H.-J.

(1996) J Am Chem Soc 118: 8791

• DOI: https://doi.org/10.1021/JA961631P

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: 6.13 kDa 
• Atom Count: 410 
• Modeled Residue Count: 27 
• Deposited Residue Count: 27 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

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

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*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-PEPTIDE LINKING	C5 H11 N O2		--
MVA	C	L-PEPTIDE LINKING	C6 H13 N O2		VAL
SAR	C	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	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-07 
Deposition Author(s): Lian, C., Robinson, H., Wang, A.H.-J.

Revision History  

• Version 1.0: 1996-12-07
  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, Other
• Version 3.0: 2024-07-10
  Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2024-11-06
  Changes: Structure summary