Research workbench
Crystal structure of the SAM-sah riboswitch with adenosine
Analyse Crystal structure of the SAM-sah riboswitch with adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YMJ
- Type
- RNA
- Length
- 208 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
- ADN, CBV, NA, MG
- Pockets
- 8 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I, M | Chains: A,C,F,I,M,O | rna | 26 | — | — |
| B, D, G, J, N, P | Chains: B,D,G,J,N,P | rna | 9 | — | — |
| C, O | Chains: A,C,F,I,M,O | rna | 25 | — | — |
Ligands and binding sites
- ADN · Adenosine · ligand · 9 copies · chains A, B, I, C, D, N, F, G, O, J, M, P
- CBV · 5-bromocytidine 5'-(dihydrogen phosphate) · ligand · 2 copies · chains C, O
- NA · Sodium ion · metal · 3 copies · chains A, M
- MG · Magnesium ion · metal · chains C
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 | 329 | 0.54 | 0.75 | 27 | ADN |
| 2 | 201 | 0.49 | 0.77 | 19 | ADN |
| 3 | 204 | 0.48 | 0.76 | 15 | ADN |
| 4 | 177 | 0.47 | 0.77 | 14 | ADN |
| 5 | 194 | 0.47 | 0.76 | 15 | ADN |
Interfaces
19 interfaces between chains.
- O–P · 495 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- C–D · 494 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- I–J · 492 Ų buried · 41 hydrogen bonds · nucleic-nucleic
- A–B · 418 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- F–G · 416 Ų buried · 32 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 6YMJ · Crystal structure of the SAM-SAH riboswitch with adenosine. · the same entry in another collection · chain O against O, 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 6YMJ · PDBe 6YMJ
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