2KMJ | pdb_00002kmj

High resolution NMR solution structure of a complex of HIV-2 TAR RNA and a synthetic tripeptide in a 1:2 stoichiometry

PDB DOI: https://doi.org/10.2210/pdb2KMJ/pdb
BMRB: 16431
NAKB: 2KMJ

Classification: RNA/PEPTIDE
Organism(s): Human immunodeficiency virus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-30 Released: 2009-08-18
Deposition Author(s): Ferner, J., Suhartono, M., Breitung, S., Jonker, H.R.A., Hennig, M., Woehnert, J., Goebel, M., Schwalbe, H.

Experimental Data Snapshot

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 10
Selection Criteria: Top-ranked ensemble

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Structures of HIV TAR RNA-ligand complexes reveal higher binding stoichiometries.

Ferner, J., Suhartono, M., Breitung, S., Jonker, H.R.A., Hennig, M., Wohnert, J., Gobel, M., Schwalbe, H.

(2009) Chembiochem 10: 1490-1494

PubMed: 19444830 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200900220
Primary Citation of Related Structures:
2KMJ

PubMed Abstract:
Target TAR by NMR: Tripeptides containing arginines as terminal residues and non-natural amino acids as central residues are good leads for drug design to target the HIV trans-activation response element (TAR). The structural characterization of the RNA-ligand complex by NMR spectroscopy reveals two specific binding sites that are located at bulge residue U23 and around the pyrimidine-stretch U40-C41-U42 directly adjacent to the bulge.

Organizational Affiliation

Institut für Organische Chemie und Chemische Biologie, Zentrum für Biomolekulare Magnetische Resonanz (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 9.96 kDa
Atom Count: 666
Modelled Residue Count: 36
Deposited Residue Count: 36
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidinylpeptide	B, C	4	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (28-MER)	A	28	Human immunodeficiency virus 2
Sequence Annotations Expand
Reference Sequence LOADING

Experimental Data & Validation

Experimental Data

Method: SOLUTION NMR
Conformers Calculated: 200
Conformers Submitted: 10
Selection Criteria: Top-ranked ensemble

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2022-03-16
Changes: Data collection, Database references, Derived calculations
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2024-11-27
Changes: Structure summary