8TWH | pdb_00008twh

Crystal structure of (GGGTT)3GGG G-quadruplex in complex with small molecule ligand RHPS4

PDB DOI: https://doi.org/10.2210/pdb8TWH/pdb
NAKB: 8TWH

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

Deposited: 2023-08-21 Released: 2024-09-04
Deposition Author(s): Yatsunyk, L.A., Martin, K.N., Lam, G.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free:
0.318 (Depositor), 0.317 (DCC)
R-Value Work:
0.295 (Depositor), 0.294 (DCC)
R-Value Observed:
0.297 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of (GGGTT)3GGG G-quadruplex in complex with small molecule ligand RHPS4

Lam, G., Martin, K.N., Yatsunyk, L.A.

To be published.

Macromolecule Content

Total Structure Weight: 61.76 kDa
Atom Count: 4,109
Modeled Residue Count: 180
Deposited Residue Count: 180
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
(GGGTT)3GGG DNA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	18	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LG1 Query on LG1 Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain LA [auth H] SDF format, chain N [auth A] SDF format, chain OA [auth I] SDF format, chain Q [auth B] SDF format, chain SA [auth J] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain SA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	BA [auth E] EA [auth F] IA [auth G] LA [auth H] N [auth A] BA [auth E], EA [auth F], IA [auth G], LA [auth H], N [auth A], OA [auth I], Q [auth B], SA [auth J], U [auth C], X [auth D]	3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM C₂₂ H₁₇ F₂ N₂ FJUYVGXXNUNWDT-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain OA [auth I] Focus chain Q [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain N [auth A] Focus chain OA [auth I] Focus chain Q [auth B] Focus chain SA [auth J] Focus chain U [auth C] Focus chain X [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain NA [auth I] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain PA [auth J] SDF format, chain QA [auth J] SDF format, chain R [auth C] SDF format, chain RA [auth J] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	AA [auth E] CA [auth F] DA [auth F] FA [auth G] GA [auth G] AA [auth E], CA [auth F], DA [auth F], FA [auth G], GA [auth G], HA [auth G], JA [auth H], K [auth A], KA [auth H], L [auth A], M [auth A], MA [auth I], NA [auth I], O [auth B], P [auth B], PA [auth J], QA [auth J], R [auth C], RA [auth J], S [auth C], T [auth C], V [auth D], W [auth D], Y [auth E], Z [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain R [auth C] Focus chain RA [auth J] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain L [auth A] Focus chain M [auth A] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain O [auth B] Focus chain P [auth B] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain R [auth C] Focus chain RA [auth J] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]