Research workbench
The leadzyme structure bound to MG(H20)6(II) at 1.8 a resolution
Analyse The leadzyme structure bound to MG(H20)6(II) at 1.8 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NUJ
- 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
- Pockets
- 7 · best druggability 0.55
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
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 | 260 | 0.55 | 0.77 | 20 | empty |
| 2 | 229 | 0.48 | 0.75 | 22 | MG |
| 3 | 208 | 0.46 | 0.75 | 22 | MG |
| 4 | 117 | 0.34 | 0.73 | 13 | MG |
| 5 | 85 | 0.32 | 0.74 | 13 | empty |
Interfaces
14 interfaces between chains.
- G–H · 506 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–B · 504 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- E–F · 487 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–D · 482 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–E · 262 Ų buried · 15 hydrogen bonds · nucleic-nucleic
Compared structures
- 1NUJ · The leadzyme structure bound to MG(H20)6(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 1NUJ · PDBe 1NUJ
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