2G5K

Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with Apramycin

PDB DOI: https://doi.org/10.2210/pdb2G5K/pdb
NAKB: 2G5K

Classification: RNA
Mutation(s): No

Deposited: 2006-02-23 Released: 2006-06-20
Deposition Author(s): Kondo, J., Francois, B., Urzhumtsev, A., Westhof, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.258

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site Complexed with Apramycin

Kondo, J., Francois, B., Urzhumtsev, A., Westhof, E.

(2006) Angew Chem Int Ed Engl 45: 3310-3314

PubMed: 16596680 Search on PubMed
DOI: https://doi.org/10.1002/anie.200600354
Primary Citation of Related Structures:
2G5K

Organizational Affiliation

Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecule Content

Total Structure Weight: 16.16 kDa
Atom Count: 1,055
Modelled Residue Count: 44
Deposited Residue Count: 46
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(UPUPGPCPGPUPCPGPCPUPCPCPGPGPAPAPAPAPGPUPCPGP*C)-3'	A, B	23	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AM2 Query on AM2 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	APRAMYCIN C₂₁ H₄₁ N₅ O₁₁ XZNUGFQTQHRASN-XQENGBIVSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AM2	PDBBind: 2G5K	Kd: 500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.270
R-Value Work: 0.258
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.123	α = 90
b = 33.123	β = 90
c = 116.421	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CrystalClear	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-06-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-06-20
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: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Structure summary

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