1A7Z

CRYSTAL STRUCTURE OF ACTINOMYCIN Z3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.097 
  • R-Value Observed: 0.080 

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 Z3
A, B
11Streptomyces fradiaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BNZ
Query on BNZ
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
BENZENE
C6 H6
UHOVQNZJYSORNB-UHFFFAOYSA-N
Modified Residues  6 Unique
IDChains TypeFormula2D DiagramParent
CTH
Query on CTH
A, B
L-PEPTIDE LINKINGC4 H8 Cl N O3THR
H5M
Query on H5M
A, B
L-PEPTIDE LINKINGC6 H11 N O3PRO
MAA
Query on MAA
A, B
L-PEPTIDE LINKINGC4 H9 N O2ALA
MVA
Query on MVA
A, B
L-PEPTIDE LINKINGC6 H13 N O2VAL
POM
Query on POM
A, B
L-PEPTIDE LINKINGC6 H9 N O3PRO
SAR
Query on SAR
A, B
PEPTIDE LINKINGC3 H7 N O2GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.097 
  • R-Value Observed: 0.080 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 14.803α = 90
b = 24.78β = 90
c = 65.059γ = 90
Software Package:
Software NamePurpose
SHELXL-97model building
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXL-97phasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1999-03-23 
    • Deposition Author(s): Schafer, M.

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