2GWA

Crystal Structure of a Complex Formed Between the DNA Holliday Junction and a Bis-Acridine Molecule.

PDB DOI: https://doi.org/10.2210/pdb2GWA/pdb
NAKB: 2GWA

Classification: DNA
Mutation(s): No

Deposited: 2006-05-04 Released: 2006-06-06
Deposition Author(s): Brogden, A.L., Hopcroft, N.H., Cardin, C.J., Searcey, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.310
R-Value Work: 0.268
R-Value Observed: 0.277

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Ligand bridging of the DNA Holliday junction: molecular recognition of a stacked-X four-way junction by a small molecule.

Brogden, A.L., Hopcroft, N.H., Searcey, M., Cardin, C.J.

(2007) Angew Chem Int Ed Engl 46: 3850-3854

PubMed: 17477457 Search on PubMed
DOI: https://doi.org/10.1002/anie.200603760
Primary Citation of Related Structures:
2GWA

Organizational Affiliation

School of Chemistry, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AD, UK.

Macromolecule Content

Total Structure Weight: 6.99 kDa
Atom Count: 573
Modelled Residue Count: 20
Deposited Residue Count: 20
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(TpCpGpGpTpApCpCpGpA)-3'	A, B	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A4C Query on A4C Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	9,9'-(HEXANE-1,6-DIYLDIIMINO)BIS{N-[2-(DIMETHYLAMINO)ETHYL]ACRIDINE-4-CARBOXAMIDE} C₄₂ H₅₀ N₈ O₂ ATHNVLFOCKEETH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density 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: 1.75 Å
R-Value Free: 0.310
R-Value Work: 0.268
R-Value Observed: 0.277
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.224	α = 90
b = 25.142	β = 110.97
c = 37.541	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
MAR345	data collection
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Advisory, Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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