MolNFT v1 · #24975 · protein + RNA
Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with C75U mutaion, in imidazole and SR2+ solution
1VC0 · Hepatitis delta virus ribozyme: “Crystal structure of the hepatitis delta virus gemonic ribozyme precursor, with C75U mutaion, in imidazole…”. X-ray diffraction, 1 ligand (SR), 5 pockets (best druggability 0.61). MolNFT v1 #24975 on…
- PDB
- 1VC0
- Type
- protein + RNA
- Length
- 168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hepatitis delta virus ribozyme; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- SR
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Hepatitis delta virus ribozyme | rna | 73 | — | — |
| A | U1 small nuclear ribonucleoprotein a | protein | 95 | 32% helix, 24% strand | P09012 |
Ligands and binding sites
- SR · Strontium ion · metal · 2 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 | 377 | 0.61 | 0.78 | 22 | SR |
| 2 | 390 | 0.54 | 0.74 | 25 | empty |
| 3 | 276 | 0.48 | 0.73 | 18 | empty |
| 4 | 114 | 0.42 | 0.77 | 18 | empty |
| 5 | 73 | 0.37 | 0.79 | 13 | SR |
Interfaces
1 interface between chains.
- B–A · 950 Ų buried · 32 hydrogen bonds · protein-nucleic
Compared structures
- 1VC0 · Crystal Structure of the Hepatitis Delta Virus Gemonic Ribozyme Precursor, with C75U… · 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 1VC0 · PDBe 1VC0 · UniProt P09012
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