Research workbench
Crystal structure of selenium-modified diels-alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
Analyse Crystal structure of selenium-modified diels-alder ribozyme complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YLS
- Type
- RNA
- Length
- 98 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA diels-alder ribozyme
- Ligands
- DAI, MG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | RNA diels-alder ribozyme | rna | 11 | — | — |
| B, D | RNA diels-alder ribozyme | rna | 38 | — | — |
Ligands and binding sites
- DAI · (3as,9as)-2-pentyl-4-hydroxymethyl-3A,4,9,9A-tetrahydro-4,9[1',2']-benzeno-1H-benz[f]isoindole-1,3(2H)-dione · ligand · 2 copies · chains A, B, D, C
- MG · Magnesium ion · metal · 13 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 603 | 0.68 | 0.78 | 33 | DAI |
| 2 | 567 | 0.61 | 0.75 | 31 | MG |
| 3 | 147 | 0.39 | 0.74 | 13 | MG |
| 4 | 135 | 0.36 | 0.73 | 15 | MG |
| 5 | 64 | 0.27 | 0.74 | 10 | MG |
Interfaces
3 interfaces between chains.
- C–D · 583 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–B · 579 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- B–D · 284 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 12 modified (nucleotide modification).
Compared structures
- 1YLS · Crystal structure of selenium-modified Diels-Alder ribozyme complexed with the product of… · 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 1YLS · PDBe 1YLS
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