3FT6

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

PDB DOI: https://doi.org/10.2210/pdb3FT6/pdb
NAKB: 3FT6

Classification: DNA
Mutation(s): No

Deposited: 2009-01-12 Released: 2010-02-02
Deposition Author(s): Maehigashi, T., Persil, O., Hud, N.V., Williams, L.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.12 ?
R-Value Free: 0.219
R-Value Work: 0.184
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

Maehigashi, T., Persil, O., Hud, N.V., Williams, L.D.

To be published.

Macromolecule Content

Total Structure Weight: 4.52 kDa
Atom Count: 330
Modelled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRL Query on PRL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	PROFLAVIN C₁₃ H₁₁ N₃ WDVSHHCDHLJJJR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	D [auth A], E [auth A], G [auth B]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.12 ?
R-Value Free: 0.219
R-Value Work: 0.184
R-Value Observed: 0.188
Space Group: P 6₅

Unit Cell:

Length ( ? )	Angle ( ? )
a = 24.563	α = 90
b = 24.563	β = 90
c = 78.276	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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3FT6

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

Crystal Structure of Proflavine in Complex with a DNA hexamer duplex

Entity ID: 1

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)