Research workbench
Crystal structure of the SAM-sah riboswitch with AMP
Analyse Crystal structure of the SAM-sah riboswitch with AMP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMK
- Type
- RNA
- Length
- 210 nucleotides
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: A,C,F,I,M,O; Chains: B,D,G,J,N,P
- Ligands
- MTA, NA, SO4
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, I, M, O | Chains: A,C,F,I,M,O | rna | 26 | — | — |
| B, D, G, J, N, P | Chains: B,D,G,J,N,P | rna | 9 | — | — |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 9 copies · chains A, B, I, C, D, N, F, G, O, J, M, P
- NA · Sodium ion · metal · 2 copies · chains D, F
- SO4 · Sulfate ion · ion · 2 copies · chains D, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.54 | 0.75 | 21 | MTA |
| 2 | 229 | 0.51 | 0.77 | 19 | MTA |
| 3 | 177 | 0.47 | 0.77 | 13 | MTA |
| 4 | 180 | 0.47 | 0.77 | 14 | MTA |
| 5 | 199 | 0.46 | 0.75 | 14 | MTA |
Interfaces
19 interfaces between chains.
- C–D · 495 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- I–J · 489 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- O–P · 486 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–B · 414 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- M–N · 413 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 6YMK · Crystal structure of the SAM-SAH riboswitch with AMP · 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 6YMK · PDBe 6YMK
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