Research workbench
Crystal structure of the methyltransferase-ribozyme 1 (with 1- benzylamine-adenosine)
Analyse Crystal structure of the methyltransferase-ribozyme 1 (with 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q7Z
- 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, MG
- Pockets
- 5 · best druggability 0.63
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
- GUN · Guanine · ligand · 2 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 723 | 0.63 | 0.74 | 39 | empty |
| 2 | 554 | 0.60 | 0.74 | 39 | empty |
| 3 | 330 | 0.52 | 0.75 | 18 | empty |
| 4 | 230 | 0.47 | 0.75 | 17 | empty |
| 5 | 88 | 0.35 | 0.76 | 18 | MG |
Interfaces
9 interfaces between chains.
- E–F · 875 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- B–C · 873 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- D–F · 654 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–C · 647 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- D–E · 468 Ų buried · 29 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7Q7Z · Crystal structure of the methyltransferase-ribozyme 1 (with 1-benzylamine-adenosine) · 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 7Q7Z · PDBe 7Q7Z
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