Research workbench
Crystal structure of squash RNA aptamer in complex with dfhbi-1T with iridium (III) ions
Analyse Crystal structure of squash RNA aptamer in complex with dfhbi-1T with iridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KVT
- Type
- RNA
- Length
- 83 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Squash RNA aptamer bound to dfhbi-1T with iridium (III) ions
- Ligands
- IRI, 2ZY, MG
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Squash RNA aptamer bound to dfhbi-1T with iridium (III) ions | rna | 83 | — | — |
Ligands and binding sites
- IRI · Iridium hexammine ion · ligand · 3 copies · chains B
- 2ZY · (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 920 | 0.69 | 0.76 | 46 | 2ZY, IRI |
| 2 | 167 | 0.38 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 7KVT · Crystal structure of Squash RNA aptamer in complex with DFHBI-1T with iridium (III) ions · the same entry in another collection · chain B against B, 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 7KVT · PDBe 7KVT
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