Research workbench
3'-deoxy modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')PPP(5')G
Analyse 3'-deoxy modification at 3' end of RNA primer complex with guanosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LNF
- Type
- RNA
- Length
- 26 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GDO))-3')
- Ligands
- GDO, GP3, MG, CO
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(GDO))-3') | rna | 13 | — | — |
Ligands and binding sites
- GDO · 3'-deoxy-guanosine 5'-monophosphate · ligand · 2 copies · chains A, B
- GP3 · Diguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies
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 | 327 | 0.49 | 0.73 | 21 | MG |
Interfaces
1 interface between chains.
- A–B · 680 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 7LNF · 3'-deoxy 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 7LNF · PDBe 7LNF
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