Research workbench
SAM-I riboswitch with a G2NA mutation in the kink turn in complex with S-adenosylmethionine
Analyse SAM-I riboswitch with a G2NA mutation in the kink turn in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YGH
- Type
- RNA
- Length
- 94 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-I riboswitch
- Ligands
- SAM, NA, K
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SAM-I riboswitch | rna | 94 | — | — |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.77 | 0.81 | 47 | SAM, NA |
| 2 | 559 | 0.66 | 0.78 | 36 | empty |
| 3 | 61 | 0.31 | 0.76 | 9 | NA |
Compared structures
- 2YGH · SAM-I riboswitch with a G2nA mutation in the Kink turn 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 2YGH · PDBe 2YGH
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