1A7Y

CRYSTAL STRUCTURE OF ACTINOMYCIN D

• PDB DOI: https://doi.org/10.2210/pdb1A7Y/pdb

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


• Deposited: 1998-03-19 Released: 1999-03-23 
• Deposition Author(s): Schafer, M., Sheldrick, G.M., Bahner, I., Lackner, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.068 
• R-Value Observed: 0.058 

Literature

Crystal Structures of Actinomycin D and Actinomycin Z3.

Schafer, M., Sheldrick, G.M., Bahner, I., Lackner, H.

(1998) Angew Chem Int Ed Engl 37: 2381-2384

• PubMed: 29710967 
• DOI: https://doi.org/10.1002/(SICI)1521-3773(19980918)37:17<2381::AID-ANIE2381>3.0.CO;2-L
• Primary Citation of Related Structures:  
  1A7Y, 1A7Z


• PubMed Abstract: 
  

  Untwinned single crystals of the actinomycins D and Z ₃ that diffracted to atomic resolution could be obtained for the first time. Low-temperature data collection and a new ab initio method for solving the structures led to precise crystal structures which showed, for example, that the unit cell of actinomycin D contains three molecules, two of which are present in the form of a hydrogen-bridged dimer related by a pseudo-twofold axis (see picture).

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Organizational Affiliation: 

Institut für Anorganische Chemie der Universität, Tammannstrasse 4, D-37077 Göttingen (Germany), Fax: [phone].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.43 kDa 
• Atom Count: 314 
• Modelled Residue Count: 33 
• Deposited Residue Count: 33 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTINOMYCIN D	A, B, C	11	Streptomyces antibioticus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EEE	D [auth A], E [auth A], F [auth A], G [auth A], H [auth C], I [auth C], J [auth C]	ETHYL ACETATE C4 H8 O2 XEKOWRVHYACXOJ-UHFFFAOYSA-N
MOH	K [auth C]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001	A, B, C	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.94 Å
• R-Value Free: 0.068 
• R-Value Observed: 0.058 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 15.737	α = 85.93
b = 15.887	β = 86.19
c = 25.156	γ = 69.86

Software Package:

Software Name	Purpose
SHELXL-97	model building
SHELXL-97	refinement
SAINT	data reduction
SADABS	data scaling
SHELXL-97	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Schafer, M., Sheldrick, G.M., Bahner, I., Lackner, H.

Revision History  

• Version 1.0: 1999-03-23
  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 1.5: 2018-03-07
  Changes: Advisory, Data collection, Other
• Version 1.6: 2019-11-13
  Changes: Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations