8TAA

Right-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin

• PDB DOI: https://doi.org/10.2210/pdb8TAA/pdb
• NAKB: 8TAA

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2023-06-27 Released: 2024-07-03 
• Deposition Author(s): Seth, P.C., Yatsunyk, L.A.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Right-left hybrid parallel G-quadruplex in complex with N-methyl mesoporphyrin

Seth, P.C., Yatsunyk, L.A.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.99 kDa 
• Atom Count: 737 
• Modelled Residue Count: 25 
• Deposited Residue Count: 25 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	A	25	Homo sapiens

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMP	D [auth A]	N-METHYLMESOPORPHYRIN C35 H40 N4 O4 YNWHQWMCLCANDI-YIYRCNGCSA-N
SPK	B [auth A]	SPERMINE (FULLY PROTONATED FORM) C10 H30 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-R
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
K	E [auth A], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.227 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.897	α = 90
b = 30.897	β = 90
c = 141.543	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHENIX	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Seth, P.C., Yatsunyk, L.A.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	1R15CA253134

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release
  
• Version 2.0: 2024-10-16
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Refinement description, Structure summary