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Hepatitis delta virus ribozyme precursor structure, with C75U mutation, bound to tl+ and cobalt hexammine (CO(NH3) 63+)
Analyse Hepatitis delta virus ribozyme precursor structure, with C75U mutation, bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OJ3
- Type
- protein + RNA
- Length
- 168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hdv ribozyme; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- NCO, TL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hdv ribozyme | rna | 73 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 95 | 31% helix, 26% strand | P09012 |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains B, A
- TL · Thallium (I) ion · metal · 9 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.65 | 0.81 | 33 | NCO |
| 2 | 429 | 0.56 | 0.75 | 27 | TL |
| 3 | 257 | 0.45 | 0.73 | 18 | TL |
| 4 | 96 | 0.43 | 0.79 | 12 | NCO |
| 5 | 90 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 970 Ų buried · 37 hydrogen bonds · protein-nucleic
Compared structures
- 2OJ3 · Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and… · the same entry in another collection · chain B against B, 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
- Every structure of UniProt P09012
- Elsewhere: RCSB PDB 2OJ3 · PDBe 2OJ3 · UniProt P09012
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