MolNFT v1 · #180284 · RNA
2'-ome modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')PPP(5')G
7KUP · 5'-R((LCC)P*(LCC)P*(LCC)P*(LCG)…: “2'-ome modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')PPP(5')G”. X-ray diffraction, 2 ligands (GP3, MG), 1 pocket (best druggability 0.50). MolNFT v1 #180284…
- PDB
- 7KUP
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R((LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(OMG))-3'
- Ligands
- GP3, MG
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-R((LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(OMG))-3' | rna | 14 | — | — |
Ligands and binding sites
- GP3 · Diguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, 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 | 354 | 0.50 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 589 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 7KUP · 2'-OMe modification at 3' end of RNA primer complex with guanosine dinucleotide ligand… · 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 7KUP · PDBe 7KUP
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.