4P1D | pdb_00004p1d

Structure of the complex of a bimolecular human telomeric DNA with Coptisine

PDB DOI: https://doi.org/10.2210/pdb4P1D/pdb
NAKB: 4P1D

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

Deposited: 2014-02-26 Released: 2015-03-18
Deposition Author(s): Ferraroni, M., Bazzicalupi, C., Gratteri, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.259 (Depositor), 0.258 (DCC)
R-Value Work:
0.232 (Depositor), 0.231 (DCC)
R-Value Observed:
0.233 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the complex of a bimolecular human telomeric DNA with Coptisine

Ferraroni, M., Bazzicalupi, C., Gratteri, P., Bilia, A.R., Sissi, C.

To be published.

Macromolecule Content

Total Structure Weight: 7.95 kDa
Atom Count: 556
Modeled Residue Count: 24
Deposited Residue Count: 24
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
telomeric DNA	A, B	12	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KPT Query on KPT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium C₁₉ H₁₄ N O₄ XYHOBCMEDLZUMP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.259 (Depositor), 0.258 (DCC)
R-Value Work: 0.232 (Depositor), 0.231 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.567	α = 90
b = 41.567	β = 90
c = 66.157	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Bazzicalupi, C.

Revision History (Full details and data files)

Version 1.0: 2015-03-18
Type: Initial release
Version 1.1: 2017-09-27
Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.