MolNFT v1 · #185687 · RNA
Crystal structure of the methyltransferase-ribozyme 1, thallium derivative (with 1-methyl-adenosine)
7Q82 · RNA 1: “Crystal structure of the methyltransferase-ribozyme 1, thallium derivative (with 1-methyl-adenosine)”. X-ray diffraction, 3 ligands (GUN, TL, MG), 3 pockets (best druggability 0.54). MolNFT v1 #185687 on GenesisL1: 3D…
- PDB
- 7Q82
- Type
- RNA
- Length
- 62 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 1; RNA 2; RNA 3
- Ligands
- GUN, TL, MG
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA 1 | rna | 14 | — | — |
| B | RNA 2 | rna | 24 | — | — |
| C | RNA 3 | rna | 24 | — | — |
Ligands and binding sites
- GUN · Guanine · ligand · chains A, B, C
- TL · Thallium (I) ion · metal · 10 copies · chains B, C, A
- MG · Magnesium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.54 | 0.74 | 30 | TL |
| 2 | 267 | 0.50 | 0.75 | 17 | TL |
| 3 | 248 | 0.46 | 0.74 | 15 | TL |
Interfaces
3 interfaces between chains.
- B–C · 913 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–C · 663 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–B · 365 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7Q82 · Crystal structure of the methyltransferase-ribozyme 1, Thallium derivative (with… · 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 7Q82 · PDBe 7Q82
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