269D | pdb_0000269d

STRUCTURAL STUDIES ON NUCLEIC ACIDS

PDB DOI: https://doi.org/10.2210/pdb269D/pdb
NAKB: 269D

Classification: DNA
Mutation(s): No

Deposited: 1996-07-12 Released: 1996-08-28
Deposition Author(s): Partridge, B.L., Salisbury, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Work:
0.180 (DCC)
R-Value Observed:
0.156 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Partridge, B.L., Salisbury, S.A.

To be published.

Macromolecule Content

Total Structure Weight: 7.8 kDa
Atom Count: 616
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
DNA (5'-D(CPGPCPGPAPAPTPTP(5CM)PGPCPG)-3')	A, B	12	N/A
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HT Query on HT Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE C₂₅ H₂₄ N₆ O INAAIJLSXJJHOZ-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Work: 0.180 (DCC)
R-Value Observed: 0.156 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.032	α = 90
b = 40.369	β = 90
c = 64.953	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement
RIGAKU	data reduction
RIGAKU	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1996-08-28

Deposition Author(s):

Partridge, B.L.

Salisbury, S.A.

Revision History (Full details and data files)

Version 1.0: 1996-08-28
Type: Initial release
Version 1.1: 2008-05-22
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2012-02-29
Changes: Other
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

Prepare Data

Validate Data

Deposit Data

Help and Resources

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