MolNFT v1 · #119051 · RNA
SAM-I riboswitch bearing the H. marismortui kt-7 variant 3BN is gu
5FKE: “SAM-I riboswitch bearing the H. marismortui kt-7 variant 3BN is gu”. X-ray diffraction, 4 ligands (SAM, BA, NA), 4 pockets (best druggability 0.79). MolNFT v1 #119051 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FKE
- 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, BA, NA, K
- Pockets
- 4 · best druggability 0.79
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
- BA · Barium ion · metal · 16 copies · chains A
- NA · Sodium ion · metal · 2 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
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.79 | 0.82 | 56 | SAM, BA, NA |
| 2 | 107 | 0.44 | 0.79 | 15 | BA, K, NA |
| 3 | 62 | 0.33 | 0.77 | 8 | BA |
| 4 | 50 | 0.26 | 0.75 | 11 | BA |
Compared structures
- 5FKE · SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is GU · 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 5FKE · PDBe 5FKE
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