Research workbench
Crystal structure of the in vitro transcribed G. kaustophilus tRNA-gly
Analyse Crystal structure of the in vitro transcribed G. kaustophilus tRNA-gly in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MGM
- Type
- RNA
- Length
- 126 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA glycine
- Ligands
- MG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA glycine | rna | 63 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 666 | 0.65 | 0.76 | 33 | MG |
| 2 | 667 | 0.65 | 0.76 | 33 | MG |
| 3 | 147 | 0.38 | 0.74 | 15 | empty |
| 4 | 123 | 0.37 | 0.74 | 15 | empty |
| 5 | 70 | 0.30 | 0.75 | 14 | MG |
Interfaces
1 interface between chains.
- A–B · 155 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Compared structures
- 4MGM · Crystal structure of the in vitro transcribed G. kaustophilus tRNA-Gly · 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 4MGM · PDBe 4MGM
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.