MolNFT v1 · #104734 · RNA
Crystal structure of the twister ribozyme with the nucleotide 5'- to the cleavage site ordered at 4.1 a resolution
4QJH: “Crystal structure of the twister ribozyme with the nucleotide 5'- to the cleavage site ordered at 4.1 a…”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.81). MolNFT v1 #104734 on GenesisL1: 3D structure, binding…
- PDB
- 4QJH
- Type
- RNA
- Length
- 222 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twister ribozyme
- Ligands
- MG
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Twister ribozyme | rna | 26 | — | — |
| B, D, F | Twister ribozyme | rna | 48 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.81 | 0.83 | 58 | MG |
| 2 | 294 | 0.67 | 0.84 | 19 | empty |
| 3 | 63 | 0.66 | 0.95 | 11 | empty |
| 4 | 320 | 0.64 | 0.81 | 19 | empty |
| 5 | 375 | 0.58 | 0.76 | 23 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1691 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- C–D · 1672 Ų buried · 130 hydrogen bonds · nucleic-nucleic
- E–F · 1661 Ų buried · 139 hydrogen bonds · nucleic-nucleic
- B–D · 427 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- A–D · 191 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 4QJH · Crystal Structure of the Twister Ribozyme with the Nucleotide 5'- to the Cleavage Site… · 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 4QJH · PDBe 4QJH
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