1M69

Atomic Resolution Structure of 5Br-9amino-DACA with d[CGTACG]2

PDB DOI: https://doi.org/10.2210/pdb1M69/pdb
NAKB: 1M69

Classification: DNA
Mutation(s): No

Deposited: 2002-07-15 Released: 2003-08-19
Deposition Author(s): Teixeira, S.C.M., Thorpe, J.H., Todd, A.K., Cardin, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.186
R-Value Work: 0.133
R-Value Observed: 0.133

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Heavy Going: the Atomic Resolution Structure of a Topoisomerase II Poison Intercalating into DNA in Multiple Orientations Also Reveals a Multiple Adenine-Thymine Hydrogen Bonding Pattern

Teixeira, S.C.M., Thorpe, J.H., Todd, A.K., Cardin, C.J.

To be published.

Macromolecule Content

Total Structure Weight: 2.79 kDa
Atom Count: 256
Modelled Residue Count: 6
Deposited Residue Count: 6
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPGPTPAPCPG)-3'	A	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DAX Query on DAX Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A]	B [auth A], C [auth A]	5-BROMO-N[2-(DIMETHYLAMINO)ETHYL]-9-AMINOACRIDINE-4-CARBOXAMIDE C₁₈ H₂₁ Br N₄ O NROQPXQSDDINMC-UHFFFAOYSA-P		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.186
R-Value Work: 0.133
R-Value Observed: 0.133
Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.186	α = 90
b = 30.186	β = 90
c = 39.443	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
SHELX	model building
SHELXL-97	refinement
XDS	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-08-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-19
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2012-02-08
Changes: Derived calculations
Version 1.4: 2017-10-11
Changes: Refinement description
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-04-03
Changes: Refinement description

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