8D79 | pdb_00008d79

Crystal structure of a four-tetrad, parallel, and Na+ stabilized Tetrahymena thermophila telomeric G-quadruplex in complex with N-methyl mesoporphyrin IX

PDB DOI: https://doi.org/10.2210/pdb8D79/pdb
NAKB: 8D79

Classification: DNA
Organism(s): Tetrahymena thermophila
Mutation(s): No

Deposited: 2022-06-07 Released: 2023-07-05
Deposition Author(s): Chen, E.V., Beseiso, D., Yatsunyk, L.A.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free:
0.253 (Depositor), 0.259 (DCC)
R-Value Work:
0.241 (Depositor), 0.249 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Biophysical and structural characterization of telomeric G-quadruplexes from Tetrahymena thermophila in complex with N-Methyl Mesoporphyrin IX

Beseiso, D., Chen, E.V., Yatsunyk, L.A.

To be published.

Macromolecule Content

Total Structure Weight: 8.59 kDa
Atom Count: 533
Modeled Residue Count: 23
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (5'-D(TPGPGPGPGPTPTPGPGPGPGPTPTPGPGPGPGPTPTPGPGPGPGPT)-3')	A	24	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MMP Query on MMP 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]	N-METHYLMESOPORPHYRIN C₃₅ H₄₀ N₄ O₄ YNWHQWMCLCANDI-YIYRCNGCSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]