Research workbench
Crystal structure of the SAM-sah riboswitch with SAM
Analyse Crystal structure of the SAM-sah riboswitch with SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLB
- 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
- SAM
- Pockets
- 8 · best druggability 0.53
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
- SAM · S-adenosylmethionine · ligand · 9 copies · chains A, B, I, C, D, N, F, G, O, J, M, P
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 | 311 | 0.53 | 0.75 | 20 | SAM |
| 2 | 215 | 0.48 | 0.76 | 19 | SAM |
| 3 | 192 | 0.48 | 0.76 | 18 | SAM |
| 4 | 200 | 0.47 | 0.76 | 18 | SAM |
| 5 | 182 | 0.47 | 0.76 | 13 | SAM |
Interfaces
19 interfaces between chains.
- C–D · 490 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- I–J · 485 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- O–P · 484 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- M–N · 409 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- F–G · 408 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 6YLB · Crystal structure of the SAM-SAH riboswitch with SAM · the same entry in another collection · chain P against P, 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 6YLB · PDBe 6YLB
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