2KXM | pdb_00002kxm

Solution NMR Structure of the 27 nucleotide engineered neomycin sensing riboswitch RNA-ribostmycin complex

PDB DOI: https://doi.org/10.2210/pdb2KXM/pdb
NAKB: 2KXM

Classification: RNA/Antibiotic
Mutation(s): No

Deposited: 2010-05-10 Released: 2011-04-20
Deposition Author(s): Duchardt-Ferner, E., Weigand, J.E., Ohlenschlager, O., Schmidtke, S.R., Suess, B., Wohnert, J.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: target function

wwPDB Validation 3D Report Full Report

Validation slider image for 2KXM

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

Literature

Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch.

Duchardt-Ferner, E., Weigand, J.E., Ohlenschlager, O., Schmidtke, S.R., Suess, B., Wohnert, J.

(2010) Angew Chem Int Ed Engl 49: 6216-6219

PubMed: 20632338 Search on PubMed
DOI: https://doi.org/10.1002/anie.201001339
Primary Citation Related Structures:
2KXM

Organizational Affiliation

Institute for Molecular Biosciences, Center for Biomolecular Magnetic Resonance (BMRZ), Johann-Wolfgang-Goethe-University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany.

Macromolecule Content

Total Structure Weight: 9.01 kDa
Atom Count: 595
Modeled Residue Count: 27
Deposited Residue Count: 27
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (27-MER)	A	27	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIO Query on RIO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RIBOSTAMYCIN C₁₇ H₃₄ N₄ O₁₀ NSKGQURZWSPSBC-VVPCINPTSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 100
Conformers Submitted: 10
Selection Criteria: target function

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-04-20

Deposition Author(s):

Duchardt-Ferner, E.

Ohlenschlager, O.

Schmidtke, S.R.

Revision History (Full details and data files)

Version 1.0: 2011-04-20
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-09-04
Changes: Structure summary
Version 1.3: 2014-02-05
Changes: Experimental preparation
Version 1.4: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.