7U38

Pixantrone tethered DNA duplex

PDB DOI: https://doi.org/10.2210/pdb7U38/pdb
NAKB: 7U38

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

Deposited: 2022-02-26 Released: 2023-03-15
Deposition Author(s): Pallan, P.S., Egli, M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.262
R-Value Work: 0.245
R-Value Observed: 0.246

wwPDB Validation 3D Report Full Report

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

Literature

Structural Characterization of a Covalent Conjugate between Pixantrone and an Abasic Site in DNA

Kellum Jr., A.H., Pallan, P.S., Terrell, J.T., Fu, Y., Noh, B., Rizzo, C.J., Egli, M., Stone, M.P.

To be published.

Macromolecule Content

Total Structure Weight: 8.05 kDa
Atom Count: 549
Modelled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Pixantrone AP conjugate-modified DNA	A, B	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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 B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	C [auth A], D [auth A], E [auth A], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.262
R-Value Work: 0.245
R-Value Observed: 0.246
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.921	α = 90
b = 95.921	β = 90
c = 73.118	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P01 CA-160032

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.