8YS7 | pdb_00008ys7

Crystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex

• PDB DOI: https://doi.org/10.2210/pdb8YS7/pdb
• NAKB: 8YS7

• Classification: DNA/ANTIBIOTIC
• Organism(s): synthetic construct, Streptomyces
• Mutation(s): No 


• Deposited: 2024-03-22 Released: 2025-04-09 
• Deposition Author(s): Lee, Y.Y., Hou, M.H.
• Funding Organization(s): Ministry of Science and Technology (MoST, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 
  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.277 (Depositor), 0.278 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of actinomycin D and Echinomycin-d(ACGGGCT/AGCCCCGT) complex

Lee, Y.Y., Hou, M.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.95 kDa 
• Atom Count: 951 
• Modeled Residue Count: 68 
• Deposited Residue Count: 68 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Echinomycin	E, H [auth A]	8	Streptomyces	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
actinomycin D	F [auth I], G [auth D]	11	Streptomyces	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*CP*CP*CP*CP*GP*T)-3')	A [auth B], C [auth K]	8	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*CP*GP*GP*GP*CP*T)-3')	B [auth C], D [auth L]	7	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QUI (Subject of Investigation/LOI)	I [auth E], J [auth E], K [auth A], L [auth A]	2-CARBOXYQUINOXALINE C9 H6 N2 O2 UPUZGXILYFKSGE-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DSN	E, H [auth A]	D-PEPTIDE LINKING	C3 H7 N O3		--
MVA	E, H [auth A]	L-PEPTIDE LINKING	C6 H13 N O2		VAL
N2C	E, H [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 S		--
NCY	E, H [auth A]	L-PEPTIDE LINKING	C4 H9 N O2 S		--
DVA	F [auth I], G [auth D]	D-PEPTIDE LINKING	C5 H11 N O2		--
SAR	F [auth I], G [auth D]	PEPTIDE LINKING	C3 H7 N O2		GLY

Biologically Interesting Molecules (External Reference) 

2 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000491	E [auth A], H [auth E]	Echinomycin	Cyclic depsipeptide / Antibiotic

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000001	F [auth D], G [auth I]	Actinomycin D	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free:  0.292 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.277 (Depositor), 0.278 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.661	α = 90
b = 132.661	β = 90
c = 50.052	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-09 
Deposition Author(s): Lee, Y.Y., Hou, M.H.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2025-04-09
  Type: Initial release