9M6E | pdb_00009m6e

Crystal structure of xanthine/guanine RNA aptamer (P1-12bp) with hypoxanthine

PDB DOI: https://doi.org/10.2210/pdb9M6E/pdb

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

Deposited: 2025-03-07 Released: 2026-09-16
Deposition Author(s): Li, M., Huang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.246 (Depositor), 0.246 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of xanthine/guanine RNA aptamer

Li, M., Huang, L.

To be published.

Macromolecule Content

Total Structure Weight: 112.75 kDa
Atom Count: 7,281
Modeled Residue Count: 328
Deposited Residue Count: 336
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (42-MER)	A [auth B] B [auth A] C [auth D] D [auth C] E A [auth B], B [auth A], C [auth D], D [auth C], E, F, G, H	42	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain Q [auth E] SDF format, chain V [auth G] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain V [auth G] mmCIF format, chain I [auth B] mmCIF format, chain M [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain V [auth G]	I [auth B], M [auth D], Q [auth E], V [auth G]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth E] Focus chain V [auth G] Interactions & Density Focus chain I [auth B] Focus chain M [auth D] Focus chain Q [auth E] Focus chain V [auth G]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth C] SDF format, chain T [auth F] SDF format, chain X [auth H] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth F] MOL2 format, chain X [auth H] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth F] mmCIF format, chain X [auth H]	K [auth A], O [auth C], T [auth F], X [auth H]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain K [auth A] Focus chain O [auth C] Focus chain T [auth F] Focus chain X [auth H] Interactions & Density Focus chain K [auth A] Focus chain O [auth C] Focus chain T [auth F] Focus chain X [auth H]
HPA (Subject of Investigation/LOI) Query on HPA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth A] SDF format, chain N [auth D] SDF format, chain P [auth C] SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain J [auth B] MOL2 format, chain L [auth A] MOL2 format, chain N [auth D] MOL2 format, chain P [auth C] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain J [auth B] mmCIF format, chain L [auth A] mmCIF format, chain N [auth D] mmCIF format, chain P [auth C] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	J [auth B] L [auth A] N [auth D] P [auth C] R [auth E] J [auth B], L [auth A], N [auth D], P [auth C], R [auth E], U [auth F], W [auth G], Y [auth H]	HYPOXANTHINE C₅ H₄ N₄ O FDGQSTZJBFJUBT-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth A] Focus chain N [auth D] Focus chain P [auth C] Focus chain R [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain J [auth B] Focus chain L [auth A] Focus chain N [auth D] Focus chain P [auth C] Focus chain R [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain S [auth E] MOL2 format, chain S [auth E] mmCIF format, chain S [auth E]	S [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain S [auth E] Interactions & Density Focus chain S [auth E]