Research workbench
Crystal structure of the corn RNA aptamer in complex with dfho, iridium hexammine soak
Analyse Crystal structure of the corn RNA aptamer in complex with dfho, iridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BJP
- Type
- RNA
- Length
- 72 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (36-mer)
- Ligands
- 747, K, IR, MG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, Y | RNA (36-mer) | rna | 36 | — | — |
Ligands and binding sites
- 747 · (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one · ligand · chains E, Y
- K · Potassium ion · metal · 4 copies · chains E, Y
- IR · Iridium ion · metal · 2 copies · chains E
- MG · Magnesium ion · metal · 2 copies · chains E
- DMS · Dimethyl sulfoxide · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.53 | 0.86 | 15 | 747 |
| 2 | 332 | 0.52 | 0.75 | 20 | IR |
| 3 | 288 | 0.48 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- E–Y · 508 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 5BJP · Crystal structure of the Corn RNA aptamer in complex with DFHO, iridium hexammine soak · the same entry in another collection · chain E against E, 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 5BJP · PDBe 5BJP
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.