MolNFT v1 · #177262 · RNA
RNA duplex containing C-ag-U
7ECP · RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3'): “RNA duplex containing C-ag-U”. X-ray diffraction, 1 ligand (AG), 2 pockets (best druggability 0.50). MolNFT v1 #177262 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7ECP
- 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*GP*CP*CP*CP*GP*GP*UP*CP*CP*C)-3')
- Ligands
- AG
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*UP*CP*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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.50 | 0.74 | 19 | empty |
| 2 | 254 | 0.46 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 555 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–B · 554 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- B–D · 91 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–C · 89 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 7ECP · RNA duplex containing C-Ag-U · 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 7ECP · PDBe 7ECP
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