2GWE | pdb_00002gwe

Crystal structure of D(G4T4G4) with six quadruplexes in the asymmetric unit.

PDB DOI: https://doi.org/10.2210/pdb2GWE/pdb
NAKB: 2GWE

Classification: DNA
Mutation(s): No

Deposited: 2006-05-04 Released: 2007-06-19
Deposition Author(s): Lee, M.P.H., Haider, S., Parkinson, G.N., Neidle, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.318 (Depositor), 0.303 (DCC)
R-Value Work:
0.223 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit.

Lee, M.P.H., Haider, S., Parkinson, G.N., Neidle, S.

To be published.

Macromolecule Content

Total Structure Weight: 46.84 kDa
Atom Count: 3,229
Modeled Residue Count: 144
Deposited Residue Count: 144
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-D(GPGPGPGPTPTPTPTPGPGPGPG)-3'	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	12	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain V [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain PA [auth L] SDF format, chain P [auth A] SDF format, chain OA [auth L] SDF format, chain O [auth A] SDF format, chain NA [auth K] SDF format, chain N [auth A] SDF format, chain MA [auth K] SDF format, chain M [auth A] SDF format, chain LA [auth K] SDF format, chain KA [auth J] SDF format, chain JA [auth J] SDF format, chain IA [auth J] SDF format, chain HA [auth I] SDF format, chain GA [auth I] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth L] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth L] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth K] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth K] MOL2 format, chain KA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain IA [auth J] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth L] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth L] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth K] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth K] mmCIF format, chain KA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain IA [auth J] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth F], BA [auth G], CA [auth G], DA [auth G], EA [auth G], FA [auth H], GA [auth I], HA [auth I], IA [auth J], JA [auth J], KA [auth J], LA [auth K], M [auth A], MA [auth K], N [auth A], NA [auth K], O [auth A], OA [auth L], P [auth A], PA [auth L], Q [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth D], W [auth E], X [auth E], Y [auth E], Z [auth F]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth K] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain OA [auth L] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth J] Focus chain LA [auth K] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain OA [auth L] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.318 (Depositor), 0.303 (DCC)
R-Value Work: 0.223 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.645	α = 90
b = 78.881	β = 90
c = 97.011	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
DENZO	data reduction
CNS	refinement
ADSC	data collection
EPMR	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-06-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-06-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2019-07-24
Changes: Data collection, Refinement description
Version 1.5: 2019-08-14
Changes: Data collection
Version 1.6: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description