386D | pdb_0000386d

THREE-DIMENSIONAL STRUCTURE AND REACTIVITY OF A PHOTOCHEMICAL CLEAVAGE AGENT BOUND TO DNA

PDB DOI: https://doi.org/10.2210/pdb386D/pdb
NAKB: 386D

Classification: DNA
Mutation(s): No

Deposited: 1998-03-11 Released: 1998-03-12
Deposition Author(s): Gasper, S.M., Armitage, B., Shui, X., Hu, G.G., Yu, C., Schuster, G., Williams, L.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.268 (Depositor)
R-Value Work:
0.196 (Depositor), 0.231 (DCC)
R-Value Observed:
0.196 (Depositor)

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Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA

Gasper, S.M., Armitage, B., Shui, X., Hu, G.G., Yu, C., Schuster, G., Williams, L.D.

(1998) J Am Chem Soc 120: 12402-12409

Macromolecule Content

Total Structure Weight: 2.21 kDa
Atom Count: 170
Modeled Residue Count: 6
Deposited Residue Count: 6
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPTPAPCPG)-3')	A	6	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AQS Query on AQS 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]	N,N-BIS(3-AMINOPROPYL)-2-ANTHRAQUINONESULFONAMIDE C₂₀ H₂₅ N₃ O₄ S HUHBNNVFLMYFIE-UHFFFAOYSA-P		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.268 (Depositor)
R-Value Work: 0.196 (Depositor), 0.231 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.02	α = 90
b = 31.02	β = 90
c = 64.91	γ = 120

Software Package:

Software Name	Purpose
MAD	model building
X-PLOR	refinement
ADSC	data collection
MAD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1998-03-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-03-12
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 2.0: 2024-02-21
Changes: Atomic model, Data collection, Database references, Derived calculations

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.