7ECK | pdb_00007eck

RNA duplex containing C-Ag-A and U-Ag-A base pairs

PDB DOI: https://doi.org/10.2210/pdb7ECK/pdb
NAKB: 7ECK

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

Deposited: 2021-03-12 Released: 2022-03-16
Deposition Author(s): Kondo, J., Uchida, Y.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.79 Å
R-Value Free:
0.291 (Depositor), 0.290 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

RNA duplex containing C-Ag-A and U-Ag-A base pairs

Kondo, J., Uchida, Y.

To be published.

Macromolecule Content

Total Structure Weight: 48.76 kDa
Atom Count: 3,045
Modeled Residue Count: 144
Deposited Residue Count: 144
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(GPGPAPCPU)-D(P(CBR))-R(PGPAPAPUPCPC)-3')	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AG (Subject of Investigation/LOI) Query on AG Download Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain X [auth G] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain GA [auth L] SDF format, chain FA [auth L] SDF format, chain EA [auth L] SDF format, chain DA [auth K] SDF format, chain CA [auth J] SDF format, chain BA [auth J] SDF format, chain AA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth G] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain GA [auth L] MOL2 format, chain FA [auth L] MOL2 format, chain EA [auth L] MOL2 format, chain DA [auth K] MOL2 format, chain CA [auth J] MOL2 format, chain BA [auth J] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth G] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain GA [auth L] mmCIF format, chain FA [auth L] mmCIF format, chain EA [auth L] mmCIF format, chain DA [auth K] mmCIF format, chain CA [auth J] mmCIF format, chain BA [auth J] mmCIF format, chain AA [auth I]	AA [auth I] BA [auth J] CA [auth J] DA [auth K] EA [auth L] AA [auth I], BA [auth J], CA [auth J], DA [auth K], EA [auth L], FA [auth L], GA [auth L], M [auth A], N [auth A], O [auth B], P [auth C], Q [auth D], R [auth D], S [auth D], T [auth E], U [auth E], V [auth F], W [auth G], X [auth G], Y [auth H], Z [auth H]	SILVER ION Ag FOIXSVOLVBLSDH-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth J] Focus chain DA [auth K] Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth J] Focus chain DA [auth K] Focus chain EA [auth L] Focus chain FA [auth L] Focus chain GA [auth L] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth H]