MolNFT v1 · #184021 · RNA
Crystal structure of the chili RNA aptamer in complex with dmhbi+
7OAW: “Crystal structure of the chili RNA aptamer in complex with dmhbi+”. X-ray diffraction, 6 ligands (GTP, V6T, SPM), 9 pockets (best druggability 0.71). MolNFT v1 #184021 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7OAW
- 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, V6T, SPM, K, MG, CL
- Pockets
- 9 · best druggability 0.71
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
- V6T · Dmhbi+ · ligand · 4 copies · chains A, C, B, D
- SPM · Spermine · ligand · chains A, C
- K · Potassium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.71 | 0.76 | 62 | K, V6T, SPM |
| 2 | 695 | 0.70 | 0.78 | 49 | K, V6T |
| 3 | 235 | 0.57 | 0.80 | 21 | K, V6T |
| 4 | 321 | 0.54 | 0.76 | 23 | empty |
| 5 | 244 | 0.52 | 0.77 | 20 | K |
Interfaces
4 interfaces between chains.
- B–D · 202 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 196 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–D · 17 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–C · 15 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7OAW · Crystal structure of the Chili RNA aptamer in complex with DMHBI+ · 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 7OAW · PDBe 7OAW
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