Download MendeleyStructural 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.
7U38 | pdb_00007u38
7U38 | pdb_00007u38
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
- 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 (Depositor), 0.270 (DCC)
- R-Value Work: 0.245 (Depositor), 0.253 (DCC)
- R-Value Observed: 0.246 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar nucleic acids by: Sequence
Entity ID: 1 | ||||
| Molecule | Chains | Length | Organism | Image |
|---|---|---|---|---|
| Pixantrone AP conjugate-modified DNA | 12 | synthetic construct |  | |
Sequence AnnotationsExpand | ||||
Reference Sequence | ||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Download:Ideal Coordinates CCD File | C [auth A], D [auth A], E [auth A], F [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.49 Å
- R-Value Free: 0.262 (Depositor), 0.270 (DCC)
- R-Value Work: 0.245 (Depositor), 0.253 (DCC)
- R-Value Observed: 0.246 (Depositor)
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 Name | Purpose |
|---|---|
| HKL-2000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data reduction |
| AutoSol | phasing |
Entry History
& Funding InformationDeposition Data
- Released Date: 2023-03-15 Deposition Author(s): Pallan, P.S., Egli, M.
| 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 - Version 2.0: 2024-05-22
Changes: Data collection, Derived calculations, Non-polymer description, Structure summary