MolNFT v1 · #167503 · RNA
Structure of the B. subtilis cobalamin riboswitch
6VMY: “Structure of the B. subtilis cobalamin riboswitch”. X-ray diffraction, 3 ligands (NCO, B1Z, MG), 9 pockets (best druggability 0.66). MolNFT v1 #167503 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VMY
- Type
- RNA
- Length
- 148 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B. subtilis cobalamin riboswitch
- Ligands
- NCO, B1Z, MG
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B. subtilis cobalamin riboswitch | rna | 148 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 7 copies · chains A
- B1Z · Adenosylcobalamin · ligand · chains A
- MG · Magnesium ion · metal · 12 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 455 | 0.66 | 0.79 | 40 | MG, NCO |
| 2 | 234 | 0.56 | 0.80 | 20 | empty |
| 3 | 277 | 0.54 | 0.77 | 19 | MG |
| 4 | 312 | 0.50 | 0.74 | 20 | MG |
| 5 | 117 | 0.40 | 0.77 | 13 | empty |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6VMY · Structure of the B. subtilis cobalamin riboswitch · 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 6VMY · PDBe 6VMY
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