9YD4 | pdb_00009yd4

RNA primer non-enzymatic extension product with DNA substrate

PDB DOI: https://doi.org/10.2210/pdb9YD4/pdb
NAKB: 9YD4

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

Deposited: 2025-09-21 Released: 2025-10-22
Deposition Author(s): Fang, Z., Szostak, J.W.
Funding Organization(s): National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.289 (Depositor), 0.286 (DCC)
R-Value Work:
0.257 (Depositor), 0.260 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Nonenzymatic RNA copying with deoxypurine

Fang, Z., Szostak, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 10.52 kDa
Atom Count: 827
Modeled Residue Count: 30
Deposited Residue Count: 30
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA/RNA (5'-R((LCC)P(LCC)P(LCC)P(LCG)PAPCPUPUPAPAPGPUPCPG)-D(P*G)-3')	A, B	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CWA (Subject of Investigation/LOI) Query on A1CWA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	(2-azanylimidazol-1-yl)-[[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy]phosphinic acid C₁₃ H₁₇ N₈ O₆ P UDDIXTSYRLRNQW-XLPZGREQSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]