MolNFT v1 · #184022 · RNA
Crystal structure of the chili RNA aptamer in complex with dmhbo+
7OAX: “Crystal structure of the chili RNA aptamer in complex with dmhbo+”. X-ray diffraction, 6 ligands (GTP, V5Z, SPM), 10 pockets (best druggability 0.68). MolNFT v1 #184022 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OAX
- Type
- RNA
- Length
- 204 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chili RNA aptamer
- Ligands
- GTP, V5Z, SPM, K, MG, CL
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Chili RNA aptamer | rna | 51 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- V5Z · Dmhbo+ · ligand · 4 copies · chains A, C, B, D
- SPM · Spermine · ligand · 4 copies · chains A, C, B, D
- K · Potassium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.68 | 0.76 | 43 | V5Z, SPM, K, GOL |
| 2 | 665 | 0.66 | 0.77 | 37 | V5Z, K |
| 3 | 266 | 0.60 | 0.80 | 22 | V5Z, K |
| 4 | 334 | 0.54 | 0.76 | 21 | empty |
| 5 | 221 | 0.54 | 0.79 | 22 | V5Z, K |
Interfaces
4 interfaces between chains.
- B–D · 198 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 197 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–D · 15 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–C · 12 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7OAX · Crystal structure of the Chili RNA aptamer in complex with DMHBO+ · 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 7OAX · PDBe 7OAX
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