Research workbench
Manganese riboswitch from xanthmonas oryzae bound to MN(II)
Analyse Manganese riboswitch from xanthmonas oryzae bound to MN(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N2V
- Type
- RNA
- Length
- 198 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- X. oryzae mn riboswitch optimized construct
- Ligands
- MG, SR, MN, NA
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | X. oryzae mn riboswitch optimized construct | rna | 99 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 39 copies · chains A, B
- SR · Strontium ion · metal · 9 copies · chains A, B
- MN · Manganese (II) ion · metal · 7 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.66 | 0.75 | 40 | SR, MG |
| 2 | 576 | 0.65 | 0.77 | 33 | MG, SR |
| 3 | 524 | 0.63 | 0.77 | 30 | MN, NA |
| 4 | 474 | 0.62 | 0.77 | 27 | MG, MN, SR |
| 5 | 273 | 0.47 | 0.74 | 21 | MG, SR |
Interfaces
1 interface between chains.
- A–B · 307 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6N2V · Manganese riboswitch from Xanthmonas oryzae bound to Mn(II) · 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 6N2V · PDBe 6N2V
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