308D | pdb_0000308d

BINDING OF DAUNOMYCIN TO B-D-GLUCOSYLATED DNA FOUND IN PROTOZOA TRYPANOSOMA BRUCEI STUDIED BY X-RAY CRYSTALLOGRAPH

PDB DOI: https://doi.org/10.2210/pdb308D/pdb
NAKB: 308D

Classification: DNA
Mutation(s): No

Deposited: 1997-01-15 Released: 1997-01-21
Deposition Author(s): Gao, Y.-G., Robinson, H., Wijsman, E.R., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.221 (Depositor)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Binding of Daunomycin to beta-D-Glucosylated DNA Found in Protozoa Trypanosoma brucei Studied by X-Ray Crystallography

Gao, Y.-G., Robinson, H., Wijsman, E.R., Van Der Marel, G.A., Van Boom, J.H., Wang, A.H.-J.

(1997) J Am Chem Soc 119: 1496-1497

Macromolecule Content

Total Structure Weight: 5.11 kDa
Atom Count: 448
Modeled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DM1 Query on DM1 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	DAUNOMYCIN C₂₇ H₂₉ N O₁₀ STQGQHZAVUOBTE-VGBVRHCVSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.221 (Depositor)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.619	α = 69.09
b = 20.096	β = 90.4
c = 26.553	γ = 108.03

Software Package:

Software Name	Purpose
ULTIMA	model building
X-PLOR	refinement
R-AXIS	data reduction
ULTIMA	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1997-01-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1997-01-21
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: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references, Structure summary
Version 1.5: 2024-04-03
Changes: Refinement description