9YRD | pdb_00009yrd

RNA oligonucleotides containing 4prime-(S)-methyl-alpha-(L)-threofuranosyl nucleic acid.

PDB DOI: https://doi.org/10.2210/pdb9YRD/pdb

Classification: RNA
Organism(s): synthetic construct
Expression System: synthetic construct
Mutation(s): No

Deposited: 2025-10-16 Released: 2026-10-21
Deposition Author(s): Harp, J.M., Egli, M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.303 (Depositor), 0.297 (DCC)
R-Value Work:
0.258 (Depositor), 0.260 (DCC)
R-Value Observed:
0.261 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9YRD

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Chiral-4prime-methyl-alpha-(L)-threofuranosyl nucleic acids (Me-TNA): Synthesis, structure, binding affinity, nuclease stability, and polymerase recognition

Mikami, A., Datta, D., Kundu, J., Kumar, V., Erande, N., Medina, E., Maola, V.A., Lee, E.M., Matsuda, S., Harp, J., Egli, M., Chaput, J.C., Manoharan, M.

To be published.

Macromolecule Content

Total Structure Weight: 7.18 kDa
Atom Count: 337
Modeled Residue Count: 10
Deposited Residue Count: 16
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA oligonucleotide	A, B	8	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
C Query on C Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
A1CY0( Subject of Investigation/LOI) Query on A1CY0 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	1-(5-deoxy-3-O-phosphono-alpha-L-arabinofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione C₁₀ H₁₅ N₂ O₈ P HRWNUYQJWGICCU-VOQBNFLRSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.303 (Depositor), 0.297 (DCC)
R-Value Work: 0.258 (Depositor), 0.260 (DCC)
R-Value Observed: 0.261 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.791	α = 90
b = 44.791	β = 90
c = 67.761	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
HKL2Map	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-10-21
Type: Initial release