MolNFT v1 · #178845 · RNA
Crystal structure of a double-ene RNA stability element in complex with a 28-mer POLY(A) RNA
7JNH: “Crystal structure of a double-ene RNA stability element in complex with a 28-mer POLY(A) RNA”. X-ray diffraction, 4 ligands (NCO, SPD, SR), 2 pockets (best druggability 0.69). MolNFT v1 #178845 on GenesisL1: 3D structure, binding…
- PDB
- 7JNH
- Type
- RNA
- Length
- 109 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28-mer POLY(A) RNA; Core double ene RNA (xtal construct) from oryza sativa…
- Ligands
- NCO, SPD, SR, MG
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 28-mer POLY(A) RNA | rna | 23 | — | — |
| B | Core double ene RNA (xtal construct) from oryza sativa TRANSPOSON,CORE double ene RNA (xtal construct) from oryza sativa transposon | rna | 86 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 12 copies · chains A, B
- SPD · Spermidine · ligand · chains B
- SR · Strontium ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.69 | 0.75 | 55 | NCO |
| 2 | 298 | 0.52 | 0.75 | 24 | NCO |
Interfaces
1 interface between chains.
- A–B · 2132 Ų buried · 141 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7JNH · Crystal structure of a double-ENE RNA stability element in complex with a 28-mer poly(A)… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 7JNH · PDBe 7JNH
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