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Crystal structure of manganese bound M-box RNA
Analyse Crystal structure of manganese bound M-box RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PDR
- Type
- RNA
- Length
- 322 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M-box riboswitch RNA
- Ligands
- MN, K
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, A | M-box riboswitch RNA | rna | 161 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 25 copies · chains X, A
- K · Potassium ion · metal · 6 copies · chains X, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.74 | 0.79 | 48 | MN |
| 2 | 606 | 0.71 | 0.80 | 49 | empty |
| 3 | 376 | 0.69 | 0.82 | 15 | empty |
| 4 | 283 | 0.63 | 0.82 | 26 | empty |
| 5 | 224 | 0.63 | 0.83 | 21 | empty |
Interfaces
1 interface between chains.
- X–A · 881 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 3PDR · Crystal structure of manganese bound M-box RNA · the same entry in another collection · chain X against X, 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 3PDR · PDBe 3PDR
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