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.

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

PubMed: 29710967 Search on PubMed
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.

Macromolecule Content

Total Structure Weight: 4.52 kDa
Atom Count: 314
Modelled Residue Count: 33
Deposited Residue Count: 33
Unique protein chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTINOMYCIN D	A, B, C	11	Streptomyces antibioticus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EEE Query on EEE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C]
MOH Query on MOH Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MVA Query on MVA	A, B, C	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on 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 Query on PRD_000001	A, B, C	Actinomycin D	Polypeptide / Antibiotic		Interactions Focus chain A Focus chain B Focus chain C Interactions & Density Focus chain A Focus chain B Focus chain C

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 1999-03-23

Deposition Author(s):

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