MolNFT v1 · #144918 · RNA
RNA-activated 2-aipg monomer, 1.5H soaking
6C8M · RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)…: “RNA-activated 2-aipg monomer, 1.5H soaking”. X-ray diffraction, 2 ligands (EQ1, EQ4), 1 pocket (best druggability 0.49). MolNFT v1 #144918 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6C8M
- Type
- RNA
- Length
- 29 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*GP*G)-3'); RNA…
- Ligands
- EQ1, EQ4
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 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*GP*G)-3') | rna | 15 | — | — |
| B | RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG) P*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3') | rna | 14 | — | — |
Ligands and binding sites
- EQ1 · [2-azanyl-3-[[(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]imidazol-1-yl]-[[(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]phosphinic acid · ligand · 2 copies · chains A, B
- EQ4 · 5'-O-[(R)-(2-amino-1H-imidazol-1-yl)(hydroxy) phosphoryl]guanosine · 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 | 337 | 0.49 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 632 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 6C8M · RNA-activated 2-AIpG monomer, 1.5h soaking · 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 6C8M · PDBe 6C8M
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