Research workbench
X-ray crystal structure of the M6C" riboswitch aptamer bound to 2- AMINOPYRIMIDO[4,5-D]PYRIMIDIN-4(3H)-one (ppao)
Analyse X-ray crystal structure of the M6C" riboswitch aptamer bound to 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LX6
- Type
- RNA
- Length
- 71 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutated adenine riboswitch aptamer
- Ligands
- 29H, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mutated adenine riboswitch aptamer | rna | 71 | — | — |
Ligands and binding sites
- 29H · 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one · ligand · chains A
- MG · Magnesium ion · metal · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.68 | 0.75 | 34 | MG |
| 2 | 348 | 0.54 | 0.75 | 28 | 29H, MG |
Compared structures
- 4LX6 · X-ray crystal structure of the M6C riboswitch aptamer bound to 2-aminopyrimido[4 · 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 4LX6 · PDBe 4LX6
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