Research workbench
Crystal structure of the SAM-sah riboswitch with sah
Analyse Crystal structure of the SAM-sah riboswitch with sah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YL5
- Type
- RNA
- Length
- 210 nucleotides
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: A,B,C,D,E,F,G,H,I,J,K,L
- Ligands
- SAH, NA, MG, SO4
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Chains: A,B,C,D,E,F,G,H,I,J,K,L | rna | 26 | — | — |
| B, D, F, H, J, L | Chains: A,B,C,D,E,F,G,H,I,J,K,L | rna | 9 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 9 copies · chains A, B, G, C, D, J, E, F, K, H, I, L
- NA · Sodium ion · metal · 14 copies · chains A, B, E, I, L
- MG · Magnesium ion · metal · 5 copies · chains A, C, D, H
- SO4 · Sulfate ion · ion · 3 copies · chains D, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.54 | 0.75 | 24 | SAH, NA |
| 2 | 218 | 0.49 | 0.76 | 20 | SAH |
| 3 | 204 | 0.48 | 0.76 | 18 | SAH, NA |
| 4 | 215 | 0.47 | 0.75 | 21 | SAH |
| 5 | 195 | 0.47 | 0.76 | 19 | SAH |
Interfaces
21 interfaces between chains.
- C–D · 485 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- G–H · 484 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- K–L · 481 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–B · 412 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- I–J · 412 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 6YL5 · Crystal structure of the SAM-SAH riboswitch with SAH · the same entry in another collection · chain J against J, 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 6YL5 · PDBe 6YL5
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