6KFL | pdb_00006kfl

Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4

PDB DOI: https://doi.org/10.2210/pdb6KFL/pdb
NAKB: 6KFL

Classification: DNA
Organism(s): Pseudorabies virus Ea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-07-08 Released: 2020-07-08
Deposition Author(s): Zhang, Y.S., Parkinson, G.N., Wei, D.G.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.218 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4

Zhang, Y.S., Parkinson, G.N., Wei, D.G.

To be published.

Macromolecule Content

Total Structure Weight: 9.72 kDa
Atom Count: 739
Modeled Residue Count: 28
Deposited Residue Count: 28
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(GPGPCPTPCPGPGPCPGPGPCPGPGPA)-3')	A, B	14	Pseudorabies virus Ea
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POH (Subject of Investigation/LOI) Query on POH Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	(1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin C₄₄ H₃₈ N₈ ABCGFHPGHXSVKI-LWQDQPMZSA-O		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NCO (Subject of Investigation/LOI) Query on NCO Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.218 (Depositor), 0.220 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.152	α = 90
b = 47.192	β = 113.15
c = 38.133	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Zhang, Y.S.

Parkinson, G.N.

Wei, D.G.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31672558

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description