MolNFT v1 · #99225 · RNA
X-ray crystal structure of the M6" riboswitch aptamer bound to PYRIMIDO[4,5-D]PYRIMIDINE-2,4-diamine (ppda)
4LX5 · Mutated adenine riboswitch aptamer: “X-ray crystal structure of the M6" riboswitch aptamer bound to PYRIMIDO[4,5-D]PYRIMIDINE-2,4-diamine (ppda)”. X-ray diffraction, 2 ligands (29G, MG), 2 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 4LX5
- 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
- 29G, 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
- 29G · pyrimido[4,5-d]pyrimidine-2,4-diamine · ligand · chains A
- MG · Magnesium ion · metal · 4 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 | 852 | 0.68 | 0.75 | 37 | MG |
| 2 | 387 | 0.55 | 0.75 | 29 | 29G, MG |
Compared structures
- 4LX5 · X-ray crystal structure of the M6 riboswitch aptamer bound to pyrimido[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 4LX5 · PDBe 4LX5
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