Download Mendeleypre-mir-125a internal loop in complex with G-clamp
Nagasawa, R., Onizuka, K., Kawamura, K., Tsuzuki, K., Murase, H., Komatsu, K.R., Miyashita, E., Saito, H., Kondo, J., Nagatsugi, F.To be published.
9J6P | pdb_00009j6p
pre-mir-125a internal loop in complex with G-clamp
- PDB DOI: https://doi.org/10.2210/pdb9J6P/pdb
- NAKB: 9J6P
- Classification: RNA
- Organism(s): synthetic construct
- Mutation(s): No
- Deposited: 2024-08-16 Released: 2025-01-15
- Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.49 Å
- R-Value Free: 0.268 (Depositor), 0.283 (DCC)
- R-Value Work: 0.200 (Depositor), 0.212 (DCC)
- R-Value Observed: 0.207 (Depositor)
Starting Model: in silico
View more details
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| RNA (5'-R(P*UP*GP*CP*GP*GP*GP*GP*UP*CP*CP*CP*GP*GP*GP*AP*GP*GP*AP*CP*CP*GP*C)-3') | 22 | synthetic construct |  | ||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| A1L3Y (Subject of Investigation/LOI) Query on A1L3Y | C [auth A], D [auth B] | ~{N}-[2-[2-[2-(2-azanylethoxy)ethoxy]ethoxy]ethyl]-2-[9-(2-azanylethoxy)-2-oxidanylidene-10~{H}-pyrimido[5,4-b][1,4]benzoxazin-3-yl]ethanamide C22 H32 N6 O7 IOPVLKFMUHLRKC-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.49 Å
- R-Value Free: 0.268 (Depositor), 0.283 (DCC)
- R-Value Work: 0.200 (Depositor), 0.212 (DCC)
- R-Value Observed: 0.207 (Depositor)
Space Group: H 3 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.156 | α = 90 |
| b = 46.156 | β = 90 |
| c = 336.178 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-01-15 Deposition Author(s): Kondo, J., Nagasawa, R., Onizuka, K., Kawamura, K., Tsuzuki, K., Murase, H., Komatsu, K.R., Miyashita, E., Saito, H., Nagatsugi, F.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Japan Agency for Medical Research and Development (AMED) | Japan | JP23ama121014 |
| Japan Science and Technology | Japan | JPMJFR2002 |
| Japan Science and Technology | Japan | JPMJSP2114 |
Revision History (Full details and data files)
- Version 1.0: 2025-01-15
Type: Initial release
