Research workbench
Crystal structure of the corn RNA aptamer in complex with dfho, site- specific 5-iodo-U
Analyse Crystal structure of the corn RNA aptamer in complex with dfho, site- specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BJO
- 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, MG
- Pockets
- 3 · best druggability 0.52
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
- MG · Magnesium ion · metal · 4 copies · chains E, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.52 | 0.74 | 21 | empty |
| 2 | 275 | 0.48 | 0.74 | 17 | MG |
| 3 | 62 | 0.47 | 0.85 | 13 | 747 |
Interfaces
1 interface between chains.
- E–Y · 511 Ų buried · 21 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5BJO · Crystal structure of the Corn RNA aptamer in complex with DFHO, site-specific 5-iodo-U · 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 5BJO · PDBe 5BJO
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