Research workbench
Crystal structure of chili RNA aptamer in complex with dmhbo+ (iridium III hexammine soaking crystal form)
Analyse Crystal structure of chili RNA aptamer in complex with dmhbo+ (iridium III… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OAV
- Type
- RNA
- Length
- 204 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chili RNA aptamer
- Ligands
- V5Z, GTP, K, IR, CL
- Pockets
- 11 · best druggability 0.63
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
- V5Z · Dmhbo+ · ligand · 4 copies · chains A, C, B, D
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 7 copies · chains A, B, C, D
- IR · Iridium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.63 | 0.77 | 36 | IR |
| 2 | 233 | 0.59 | 0.81 | 19 | V5Z |
| 3 | 254 | 0.58 | 0.79 | 20 | V5Z |
| 4 | 236 | 0.57 | 0.80 | 20 | V5Z, K |
| 5 | 180 | 0.57 | 0.82 | 17 | V5Z |
Interfaces
3 interfaces between chains.
- B–D · 240 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 240 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- C–D · 13 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7OAV · Crystal structure of Chili RNA aptamer in complex with DMHBO+ (Iridium III hexammine… · 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 7OAV · PDBe 7OAV
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