Research workbench
Crystal Structure of the HCV IRES pseudoknot domain
Analyse Crystal Structure of the HCV IRES pseudoknot domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T4B
- Type
- RNA
- Length
- 84 nucleotides
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.55
- Molecule
- HCV IRES pseudoknot domain plus crystallization module
- Ligands
- NI
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · resolution 3.55 · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HCV IRES pseudoknot domain plus crystallization module | rna | 84 | — | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 17 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.49 | 0.76 | 19 | NI |
| 2 | 328 | 0.48 | 0.72 | 23 | NI |
| 3 | 175 | 0.41 | 0.74 | 15 | NI |
| 4 | 145 | 0.36 | 0.73 | 18 | NI |
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3T4B · Crystal structure of the HCV ires pseudoknot domain · 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 3T4B · PDBe 3T4B
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