1ZZ5 | pdb_00001zz5

Molecular Recognition of RNA by Neomycin and a Restricted Neomycin Derivative

PDB DOI: https://doi.org/10.2210/pdb1ZZ5/pdb
NAKB: 1ZZ5

Classification: RNA
Mutation(s): No

Deposited: 2005-06-13 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: 3.00 Å
R-Value Free:
0.281 (Depositor), 0.282 (DCC)
R-Value Work:
0.233 (Depositor), 0.234 (DCC)

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 kDa
Atom Count: 1,419
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

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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
CNY Query on CNY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	F [auth A], G [auth A], H [auth C], I [auth C]	13,15-DIAMINO-2-(AMINOMETHYL)-3,4,9,12-TETRAHYDROXYHEXADECAHYDRO-2H-7,10-EPOXYPYRANO[2,3-B][1,10,4]BENZODIOXAZACYCLODODECIN-8-YL 2,6-DIAMINO-2,6-DIDEOXYHEXOPYRANOSIDE C₂₃ H₄₄ N₆ O₁₂ DXIORKRGAWCDSD-LSWIJEOBSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth D]	E [auth A], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.281 (Depositor), 0.282 (DCC)
R-Value Work: 0.233 (Depositor), 0.234 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.74	α = 90
b = 50.75	β = 90
c = 144.72	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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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