MolNFT v1 · #28656 · RNA
Crystal structure of the diels-alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene
1YKV: “Crystal structure of the diels-alder ribozyme complexed with the product of the reaction between…”. X-ray diffraction, 2 ligands (DAI, MG), 6 pockets (best druggability 0.67). MolNFT v1 #28656 on GenesisL1: 3D structure, binding…
- PDB
- 1YKV
- Type
- RNA
- Length
- 98 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diels-alder ribozyme
- Ligands
- DAI, MG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Diels-alder ribozyme | rna | 11 | — | — |
| B, D | 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 · 7 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.67 | 0.78 | 29 | DAI |
| 2 | 567 | 0.61 | 0.75 | 30 | MG |
| 3 | 135 | 0.36 | 0.73 | 15 | empty |
| 4 | 104 | 0.31 | 0.72 | 13 | empty |
| 5 | 70 | 0.30 | 0.75 | 11 | MG |
Interfaces
3 interfaces between chains.
- A–B · 566 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- C–D · 558 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- B–D · 276 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 1YKV · Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction… · 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 1YKV · PDBe 1YKV
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