36LE | pdb_000036le

RNA-dGMP complex with L-G-terminal primer

PDB DOI: https://doi.org/10.2210/pdb36LE/pdb

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

Deposited: 2026-06-16 Released: 2026-07-01
Deposition Author(s): Essex, J., Szostak, J.W.
Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.259 (Depositor), 0.263 (DCC)
R-Value Work:
0.224 (Depositor), 0.227 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Effects of Chemically Activated L-Nucleotides on Nonenzymatic RNA Copying

Essex, J., Jia, X., Zhang, J., Szostak, J.W.

To be published.

Macromolecule Content

Total Structure Weight: 22.67 kDa
Atom Count: 1,429
Modeled Residue Count: 52
Deposited Residue Count: 56
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (16-mer)	A, B, C, D	14	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0G (Subject of Investigation/LOI) Query on 0G Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain P [auth D] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain P [auth D] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain P [auth D] mmCIF format, chain E [auth A]	E [auth A], H [auth B], K [auth C], P [auth D]	L-GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-GIMIYPNGSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain P [auth D]
DGP Query on DGP Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain M [auth C] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain M [auth C] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain M [auth C] mmCIF format, chain F [auth A]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], Q [auth D], R [auth D]	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P LTFMZDNNPPEQNG-KVQBGUIXSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	N [auth C], O [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain N [auth C] Focus chain O [auth C] Focus chain S [auth D]