MolNFT v1 · #135957 · RNA
RNA primer-template complex with guanosine dinucleotide G(5')PPPP(5')G ligand
5UEG · RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*…: “RNA primer-template complex with guanosine dinucleotide G(5')PPPP(5')G ligand”. X-ray diffraction, 1 ligand (86P), 2 pockets (best druggability 0.49). MolNFT v1 #135957…
- PDB
- 5UEG
- Type
- RNA
- Length
- 56 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3')
- Ligands
- 86P
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- 86P · [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R}, 3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.49 | 0.73 | 19 | empty |
| 2 | 307 | 0.48 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 585 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–B · 584 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–C · 82 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (nucleotide modification).
Compared structures
- 5UEG · RNA primer-template complex with guanosine dinucleotide G(5')pppp(5')G 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 5UEG · PDBe 5UEG
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