2A04 | pdb_00002a04

Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

PDB DOI: https://doi.org/10.2210/pdb2A04/pdb
NAKB: 2A04

Classification: RNA
Mutation(s): No

Deposited: 2005-06-15 Released: 2005-09-20
Deposition Author(s): Zhao, Q., Zhao, F., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.318 (Depositor), 0.317 (DCC)
R-Value Work:
0.254 (Depositor), 0.258 (DCC)
R-Value Observed:
0.298 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Molecular recognition of RNA by neomycin and a restricted neomycin derivative

Zhao, F., Zhao, Q., Blount, K.F., Han, Q., Tor, Y., Hermann, T.

(2005) Angew Chem Int Ed Engl 44: 5329-5334

PubMed: 16037995 Search on PubMed
DOI: https://doi.org/10.1002/anie.200500903
Primary Citation Related Structures:
1ZX7, 1ZZ5, 2A04

Organizational Affiliation

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, 92093, USA.

Macromolecule Content

Total Structure Weight: 21.08 kDa
Atom Count: 1,418
Modeled Residue Count: 58
Deposited Residue Count: 58
Unique nucleic acid chains: 2

Macromolecules

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Molecule	Chains	Length	Organism
Entity ID: 1
5'-R(GPUPGPGPUPGPAPAPGPUPCPGPCPGP*G)-3'	A, C	15	N/A
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
5'-R(CPGPCPGPUPCPAPCPAPCPCPAPCPC)-3'	B, D	14	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMY Query on NMY Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain I [auth C]	E [auth A], F [auth A], H [auth C], I [auth C]	NEOMYCIN C₂₃ H₄₆ N₆ O₁₃ PGBHMTALBVVCIT-VCIWKGPPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth C] Focus chain I [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth C]	G [auth A], J [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.318 (Depositor), 0.317 (DCC)
R-Value Work: 0.254 (Depositor), 0.258 (DCC)
R-Value Observed: 0.298 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.8	α = 90
b = 49.9	β = 90
c = 144.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-09-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-09-20
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations