MolNFT v1 · #113969 · RNA
Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of HG(II)
5AY4 · RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3'): “Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of HG(II)”. X-ray diffraction, 1 ligand (NA), 1 pocket (best druggability 0.34). MolNFT v1…
- PDB
- 5AY4
- Type
- RNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3')
- Ligands
- NA
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.34 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 47 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5AY4 · Crystal structure of RNA duplex containing C-C base pairs obtained in the presence of… · 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 5AY4 · PDBe 5AY4
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