MolNFT v1 · #113967 · RNA
Crystal structure of RNA duplex containing C-AG(I)-C base pairs
5AY2 · RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3'): “Crystal structure of RNA duplex containing C-AG(I)-C base pairs”. X-ray diffraction, 1 ligand (AG), 3 pockets (best druggability 0.52). MolNFT v1 #113967 on GenesisL1: 3D…
- PDB
- 5AY2
- Type
- RNA
- Length
- 48 nucleotides
- Chains
- 4
- 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
- AG
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*AP*CP*UP*CP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- AG · Silver ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.52 | 0.75 | 20 | empty |
| 2 | 309 | 0.50 | 0.74 | 18 | empty |
| 3 | 72 | 0.32 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- C–D · 540 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 537 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–D · 129 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–C · 127 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–C · 96 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 5AY2 · Crystal structure of RNA duplex containing C-Ag(I)-C base pairs · 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 5AY2 · PDBe 5AY2
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