ISDA

Deposition Date 2009-03-18

Release Date 2009-03-31

Last Version Date 2025-03-26

Entry Detail

PDB ID:

3GO3

Keywords:

DNA/ANTIBIOTIC

Title:

Interactions of an echinomycin-DNA complex with manganese(II) ions

Biological Source:

Source Organism:

STREPTOMYCES ECHINATUS (Taxon ID: 67293)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.10 Å

R-Value Free:

0.19

R-Value Observed:

0.16

Space Group:

P 41 21 2

Download Validation Report

Macromolecular Entities

Polymer Type:polypeptide(L)
Molecule:ECHINOMYCIN
Chain IDs:C, D
Chain Length:8
Number of Molecules:2
Biological Source:STREPTOMYCES ECHINATUS

Ligand Molecules

PEG

QUI

Peptide-like Molecules

PRD_000491

Primary Citation

Interaction of an Echinomycin-DNA Complex with Manganese Ion

Pfoh, R, Cuesta-Seijo, J.A, Sheldrick, G.M.Show

Acta Crystallogr.,Sect.F 65 660 ? (2009)

PMID: 19574634 DOI: 10.1107/S1744309109019654

Abstact

The crystal structure of an echinomycin-d(ACGTACGT) duplex interacting with manganese(II) was solved by Mn-SAD using in-house data and refined to 1.1 A resolution against synchrotron data. This complex crystallizes in a different space group compared with related complexes and shows a different mode of base pairing next to the bis-intercalation site, suggesting that the energy difference between Hoogsteen and Watson-Crick pairing is rather small. The binding of manganese to N7 of guanine is only possible because of DNA unwinding induced by the echinomycin, which might help to explain the mode of action of the drug.

Legend

Protein

Chemical

Disease

Primary Citation of related structures