Research workbench
Co-crystal structure of the G. kaustophilus glyqs T box riboswitch stem I in complex with tRNA
Analyse Co-crystal structure of the G. kaustophilus glyqs T box riboswitch stem I in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MGN
- Type
- RNA
- Length
- 317 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyqs T box riboswitch; TRNA-glycine
- Ligands
- MG
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glyqs T box riboswitch | rna | 86 | — | — |
| B | TRNA-glycine | rna | 72 | — | — |
| D | TRNA-glycine | rna | 73 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 18 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.71 | 0.78 | 43 | MG |
| 2 | 876 | 0.69 | 0.76 | 40 | MG |
| 3 | 744 | 0.66 | 0.76 | 33 | MG |
| 4 | 339 | 0.58 | 0.77 | 24 | MG |
| 5 | 350 | 0.57 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 903 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 870 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–D · 357 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4MGN · Co-crystal structure of the G. kaustophilus glyQS T box riboswitch Stem I in complex 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 4MGN · PDBe 4MGN
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