MolNFT v1 · #49660 · RNA
Hammerhead ribozyme G12A mutant after cleavage
2QUW · Hammerhead ribozyme, cleaved fragment: “Hammerhead ribozyme G12A mutant after cleavage”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.59). MolNFT v1 #49660 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2QUW
- Type
- RNA
- Length
- 138 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hammerhead ribozyme, cleaved fragment
- Ligands
- MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hammerhead ribozyme, cleaved fragment | rna | 12 | — | — |
| B, D | Hammerhead ribozyme, cleaved fragment | rna | 57 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 17 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 597 | 0.59 | 0.74 | 29 | MG |
| 2 | 457 | 0.59 | 0.76 | 30 | MG |
| 3 | 489 | 0.55 | 0.73 | 30 | MG |
| 4 | 353 | 0.49 | 0.73 | 23 | empty |
| 5 | 135 | 0.36 | 0.73 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 823 Ų buried · 69 hydrogen bonds · nucleic-nucleic
- C–D · 820 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- B–D · 275 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 189 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–D · 29 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 2QUW · Hammerhead Ribozyme G12A mutant after cleavage · 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 2QUW · PDBe 2QUW
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