MolNFT v1 · #177257 · RNA
RNA duplex containing C-ag-a and U-ag-a base pairs
7ECK · DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))…: “RNA duplex containing C-ag-a and U-ag-a base pairs”. X-ray diffraction, 1 ligand (AG), 4 pockets (best druggability 0.54). MolNFT v1 #177257 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7ECK
- Type
- RNA
- Length
- 144 nucleotides
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))- R(P*GP*AP*AP*UP*CP*C)-3')
- Ligands
- AG
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | DNA/RNA (5'-R(*GP*GP*AP*CP*U)-D(P*(CBR))- R(P*GP*AP*AP*UP*CP*C)-3') | rna | 12 | — | — |
Ligands and binding sites
- AG · Silver ion · metal · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.54 | 0.74 | 29 | empty |
| 2 | 55 | 0.28 | 0.75 | 10 | empty |
| 3 | 56 | 0.28 | 0.75 | 10 | empty |
| 4 | 60 | 0.27 | 0.74 | 9 | empty |
Interfaces
30 interfaces between chains.
- A–B · 553 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- C–D · 542 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- G–H · 537 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- I–J · 535 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- E–F · 534 Ų buried · 50 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (nucleotide modification).
Compared structures
- 7ECK · RNA duplex containing C-Ag-A and U-Ag-A 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 7ECK · PDBe 7ECK
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