2NOK | pdb_00002nok

Crystal Structure of an RNA domain from Hepatitis C virus.

PDB DOI: https://doi.org/10.2210/pdb2NOK/pdb
NAKB: 2NOK

Classification: RNA
Mutation(s): No

Deposited: 2006-10-25 Released: 2007-02-13
Deposition Author(s): Dibrov, S.M., Johnston-Cos, H., Weng, Y.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.302 (Depositor), 0.310 (DCC)
R-Value Work:
0.257 (Depositor), 0.263 (DCC)
R-Value Observed:
0.259 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution.

Dibrov, S.M., Johnston-Cox, H., Weng, Y.H., Hermann, T.

(2007) Angew Chem Int Ed Engl 46: 226-229

PubMed: 17131443 Search on PubMed
DOI: https://doi.org/10.1002/anie.200603807
Primary Citation Related Structures:
2NOK

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Macromolecule Content

Total Structure Weight: 28.57 kDa
Atom Count: 1,869
Modeled Residue Count: 88
Deposited Residue Count: 88
Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
5'-R(CPGPGPAPGPGPAPAPCPUPAPCPUPGPUPCPUPUPCPAPCPGPCPC)-3'	A, C	24	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
5'-R(GPCPGPUPGPUPCPGPUPGPCPAPGPCPCPUPCPCPGPG)-3'	B, D	20	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	F [auth A], G [auth A], M [auth C], N [auth C], O [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	E [auth A] H [auth B] I [auth B] J [auth B] K [auth B] E [auth A], H [auth B], I [auth B], J [auth B], K [auth B], L [auth C], P [auth D], Q [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth C] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.302 (Depositor), 0.310 (DCC)
R-Value Work: 0.257 (Depositor), 0.263 (DCC)
R-Value Observed: 0.259 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.098	α = 90
b = 65.351	β = 90
c = 92.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-02-13

Deposition Author(s):

Dibrov, S.M.

Johnston-Cos, H.

Weng, Y.H.

Revision History (Full details and data files)

Version 1.0: 2007-02-13
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: 2023-12-27
Changes: Data collection, Database references, Derived calculations