Research workbench
DNA modification at 3' end of RNA primer complex with guanosine dinucleotide ligand G(5')PPP(5')G
Analyse DNA 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
- 7KUL
- Type
- RNA
- Length
- 28 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3')
- Ligands
- GP3, MG
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA/RNA (5'-R(*(LKC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*C)-D(P*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- GP3 · Diguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 12 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.51 | 0.73 | 22 | MG |
Interfaces
1 interface between chains.
- A–B · 588 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 7KUL · DNA 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 7KUL · PDBe 7KUL
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