3GO3 | pdb_00003go3

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

PDB DOI: https://doi.org/10.2210/pdb3GO3/pdb
NAKB: 3GO3

Classification: DNA/ANTIBIOTIC
Organism(s): Streptomyces echinatus
Mutation(s): Yes

Deposited: 2009-03-18 Released: 2009-03-31
Deposition Author(s): Pfoh, R., Cuesta-Seijo, J.A., Sheldrick, G.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.196 (Depositor), 0.225 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Interaction of an Echinomycin-DNA Complex with Manganese Ion

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

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 660

PubMed: 19574634 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309109019654
Primary Citation Related Structures:
3GO3

PubMed Abstract:
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.

Organizational Affiliation

Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 7.38 kDa
Atom Count: 565
Modeled Residue Count: 36
Deposited Residue Count: 36
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ECHINOMYCIN	C, D	8	Streptomyces echinatus	Mutation(s): 2

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(APCPGPTPAPCPGPT)-3'	A, B	8	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QUI Query on QUI Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain H [auth C]	H [auth C], I [auth C], J [auth D], K [auth D]	2-CARBOXYQUINOXALINE C₉ H₆ N₂ O₂ UPUZGXILYFKSGE-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DSN Query on DSN	C, D	D-PEPTIDE LINKING	C₃ H₇ N O₃		--
MVA Query on MVA	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
N2C Query on N2C	C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ S		--
NCY Query on NCY	C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂ S		--

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000491 Query on PRD_000491	C, D	Echinomycin	Cyclic depsipeptide / Antibiotic		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.196 (Depositor), 0.225 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.544	α = 90
b = 26.544	β = 90
c = 162.129	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHELXL-97	refinement
XDS	data reduction
SAINT	data reduction
SADABS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Pfoh, R.

Cuesta-Seijo, J.A.

Sheldrick, G.M.

Revision History (Full details and data files)

Version 1.0: 2009-03-31
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: 2025-03-26
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary