MolNFT v1 · #16304 · RNA
The leadzyme ribozyme bound to MG(H2O)6(II) and SR(II) at 1.8 a resolution
1NUV · 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3': “The leadzyme ribozyme bound to MG(H2O)6(II) and SR(II) at 1.8 a resolution”. X-ray diffraction, 2 ligands (MG, SR), 7 pockets (best druggability 0.56). MolNFT v1 #16304 on GenesisL1…
- PDB
- 1NUV
- Type
- RNA
- Length
- 96 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3'; 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3'
- Ligands
- MG, SR
- Pockets
- 7 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | 5'-R(*CP*GP*GP*AP*CP*CP*GP*AP*GP*CP*CP*AP*G)-3' | rna | 13 | — | — |
| B, D, F, H | 5'-R(*GP*CP*UP*GP*GP*GP*AP*GP*UP*CP*C)-3' | rna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 10 copies · chains A, B, C, D, E, F, G, H
- SR · Strontium ion · metal · 6 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.56 | 0.77 | 22 | SR |
| 2 | 233 | 0.49 | 0.76 | 22 | MG, SR |
| 3 | 232 | 0.48 | 0.75 | 22 | MG, SR |
| 4 | 135 | 0.37 | 0.73 | 18 | empty |
| 5 | 122 | 0.34 | 0.73 | 13 | MG |
Interfaces
14 interfaces between chains.
- G–H · 515 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–B · 511 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- E–F · 492 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 492 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- C–E · 254 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 1NUV · The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A resolution · 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 1NUV · PDBe 1NUV
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