MolNFT v1 · #104730 · RNA
Crystal structure of twister with the nucleotide 5'- to the cleavage site disordered at 3.1 a resolution
4QJD · Twister RNA sequence: “Crystal structure of twister with the nucleotide 5'- to the cleavage site disordered at 3.1 a resolution”. X-ray diffraction, 1 ligand (MG), 16 pockets (best druggability 0.71). MolNFT v1 #104730 on GenesisL1…
- PDB
- 4QJD
- Type
- RNA
- Length
- 288 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Twister RNA sequence
- Ligands
- MG
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Twister RNA sequence | rna | 24 | — | — |
| B, D, F, H | Twister RNA sequence | rna | 47 | — | — |
| C, G | Twister RNA sequence | rna | 25 | — | — |
| E | Twister RNA sequence | rna | 26 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.71 | 0.77 | 42 | empty |
| 2 | 1058 | 0.70 | 0.76 | 44 | empty |
| 3 | 874 | 0.69 | 0.76 | 44 | empty |
| 4 | 842 | 0.69 | 0.76 | 36 | empty |
| 5 | 462 | 0.58 | 0.75 | 24 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1430 Ų buried · 101 hydrogen bonds · nucleic-nucleic
- E–F · 1378 Ų buried · 85 hydrogen bonds · nucleic-nucleic
- C–D · 1346 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–B · 1302 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- B–D · 378 Ų buried · 26 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4QJD · Crystal Structure of Twister with the Nucleotide 5'- to the Cleavage Site Disordered at… · 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 4QJD · PDBe 4QJD
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