Research workbench
Crystal structure of the methyltransferase-ribozyme 1, no magnesium condition (with 1-methyl-adenosine)
Analyse Crystal structure of the methyltransferase-ribozyme 1, no magnesium condition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q80
- Type
- RNA
- Length
- 124 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 1; RNA 2; RNA 3
- Ligands
- GUN, NA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | RNA 1 | rna | 14 | — | — |
| B, E | RNA 2 | rna | 24 | — | — |
| C, F | RNA 3 | rna | 24 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.57 | 0.74 | 30 | empty |
| 2 | 390 | 0.52 | 0.73 | 33 | empty |
| 3 | 288 | 0.49 | 0.74 | 15 | empty |
| 4 | 228 | 0.47 | 0.75 | 15 | empty |
| 5 | 184 | 0.43 | 0.74 | 18 | empty |
Interfaces
9 interfaces between chains.
- B–C · 880 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- E–F · 871 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- D–F · 643 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–C · 625 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- D–E · 381 Ų buried · 31 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7Q80 · Crystal structure of the methyltransferase-ribozyme 1, no Magnesium condition (with… · the same entry in another collection · chain C against C, 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 7Q80 · PDBe 7Q80
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