8VOE | pdb_00008voe

The DNA 16-mer sequence 5'-GCTGGATTAATCCAGC-3' bound by a DB1992 stacked dimer

PDB DOI: https://doi.org/10.2210/pdb8VOE/pdb
NAKB: 8VOE

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2024-01-15 Released: 2025-01-22
Deposition Author(s): Terrell, J.R., Wilson, W.D.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.271 (Depositor), 0.273 (DCC)
R-Value Work:
0.249 (Depositor), 0.251 (DCC)
R-Value Observed:
0.252 (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

Structural Examination of DNA Minor Groove Binding by Diamidine Stacked Dimers

Terrell, J.R., Paul, A., Ogbonna, E.N., Farahat, A.A., Wilson, W.D.

To be published.

Macromolecule Content

Total Structure Weight: 5.53 kDa
Atom Count: 375
Modeled Residue Count: 16
Deposited Residue Count: 16
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(GPCPTPGPGPAPTPTPAPAPTPCPCPAPGPC)-3')	A	16	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AB3 (Subject of Investigation/LOI) Query on A1AB3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(2M)-2-[(5P)-5-(5-carbamimidoylthiophen-2-yl)furan-2-yl]-1H-benzimidazole-6-carboximidamide C₁₇ H₁₄ N₆ O S UUWSLLFRNHISGE-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]