217D

CRYSTAL STRUCTURES OF THE B-FORM DNA-RNA CHIMER (5'-D(IP)-R(CP)-D(IP)-R(CP)-D(IPCPIPC)-3') COMPLEXED WITH DISTAMYCIN

PDB DOI: https://doi.org/10.2210/pdb217D/pdb
NAKB: 217D

Classification: DNA-RNA HYBRID
Mutation(s): No

Deposited: 1995-07-18 Released: 1996-01-29
Deposition Author(s): Chen, X., Ramakrishnan, B., Sundaralingam, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Work: 0.159
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of B-form DNA-RNA chimers complexed with distamycin.

Chen, X., Ramakrishnan, B., Sundaralingam, M.

(1995) Nat Struct Biol 2: 733-735

PubMed: 7552741 Search on PubMed
DOI: https://doi.org/10.1038/nsb0995-733
Primary Citation of Related Structures:
216D, 217D

PubMed Abstract:
Two DNA-RNA chimers, complexed with DNA minor groove binding drugs, have been observed to adopt the B-form conformation for the first time. Thus, the RNA duplex may assume the B-DNA conformation when interacting with drugs, peptides or proteins.

Macromolecule Content

Total Structure Weight: 2.91 kDa
Atom Count: 240
Modelled Residue Count: 8
Deposited Residue Count: 8
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D(IP)-R(CP)-D(IP)-R(CP)-D(IPCPIPC)-3')	A	8	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DMY Query on DMY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	DISTAMYCIN A C₂₂ H₂₇ N₉ O₄ UPBAOYRENQEPJO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 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: 1.70 Å
R-Value Work: 0.159
R-Value Observed: 0.159
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.93	α = 90
b = 27.93	β = 90
c = 57.47	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1996-01-29

Deposition Author(s):

Chen, X.

Ramakrishnan, B.

Sundaralingam, M.

Revision History (Full details and data files)

Version 1.0: 1996-01-29
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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217D

CRYSTAL STRUCTURES OF THE B-FORM DNA-RNA CHIMER (5'-D(*IP*)-R(*CP*)-D(*IP*)-R(*CP*)-D(*IP*CP*IP*C)-3') COMPLEXED WITH DISTAMYCIN