2IE1 | pdb_00002ie1

Polyamines stabilize left-handed Z-DNA. We found new type of polyamine which stabilize left-handed Z-DNA by X-ray crystallography

PDB DOI: https://doi.org/10.2210/pdb2IE1/pdb
NAKB: 2IE1

Classification: DNA
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2006-09-16 Released: 2007-10-09
Deposition Author(s): Ohishi, H., Odoko, M., Tsukamoto, K., Hiyama, Y., Maezaki, N., Grzeskowiak, K., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.205 (Depositor)
R-Value Work:
0.190 (Depositor), 0.254 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Polyamines stabilize left-handed Z-DNA. We found new type of polyamine which stabilize left-handed Z-DNA by X-ray crystallography

Ohishi, H., Odoko, M., Tsukamoto, K., Hiyama, Y., Maezaki, N., Grzeskowiak, K., Ishida, T., Tanaka, T., Okabe, N., Fukuyama, K.

To be published.

Macromolecule Content

Total Structure Weight: 4 kDa
Atom Count: 321
Modeled Residue Count: 12
Deposited Residue Count: 12
Unique nucleic acid chains: 1

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(DCPDGPDCPDGPDCPDG)-3')	A, B	6	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PAW Query on PAW Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	N-(2-AMINOETHYL)-N'-{2-[(2-AMINOETHYL)AMINO]ETHYL}ETHANE-1,2-DIAMINE C₈ H₂₃ N₅ FAGUFWYHJQFNRV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.205 (Depositor)
R-Value Work: 0.190 (Depositor), 0.254 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 17.64	α = 90
b = 30.38	β = 90
c = 43.63	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MERLOT	phasing
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-10-09

Deposition Author(s):

Grzeskowiak, K.

Revision History (Full details and data files)

Version 1.0: 2007-10-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-11-29
Changes: Database references, Source and taxonomy

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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.