Research workbench
TNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')ppp(5')G
Analyse TNA modification at 3' end of RNA primer complex with guanosine dinucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LNG
- Type
- RNA
- Length
- 25 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Molecule
- RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(TG))-3')
- Ligands
- TG, GP3, LCG
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(TG))-3') | rna | 14 | — | — |
| B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*(TG))-3') | rna | 11 | — | — |
Ligands and binding sites
- TG · 2-azanyl-9-[(2~{R},3~{R},4~{S})-3-oxidanyl-4-[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxy-oxolan-2-yl]-1~{H}-purin-6-one · ligand · 2 copies · chains A, B
- GP3 · Diguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- LCG · [(1R,3R,4R,7S)-7-hydroxy-3-(guanin-9-yl)-2,5-dioxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate · ligand · 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 | 287 | 0.48 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 557 Ų buried · 45 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 7 modified, 4 covalent (nucleotide modification, covalent ligand).
Compared structures
- 7LNG · Tna 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 7LNG · PDBe 7LNG
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