1A7Y

CRYSTAL STRUCTURE OF ACTINOMYCIN D


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history


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

  • 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).


  • Organizational Affiliation

    Institut für Anorganische Chemie der Universität, Tammannstrasse 4, D-37077 Göttingen (Germany), Fax: (+49) 551-392-582.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACTINOMYCIN D
A, B, C
11Streptomyces antibioticusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EEE
Query on EEE

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth C]
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
Query on MOH

Download Ideal Coordinates CCD File 
K [auth C]METHANOL
C H4 O
OKKJLVBELUTLKV-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MVA
Query on MVA
A, B, C
L-PEPTIDE LINKINGC6 H13 N O2VAL
SAR
Query on SAR
A, B, C
PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
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 = 15.737α = 85.93
b = 15.887β = 86.19
c = 25.156γ = 69.86
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 3.0: 2024-07-10
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary