Research workbench
Hepatitis delta virus gemonic ribozyme precursor, with MG2+ bound
Analyse Hepatitis delta virus gemonic ribozyme precursor, with MG2+ bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SJ3
- Type
- protein + RNA
- Length
- 168 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precursor form of the hepatitis delta virus ribozyme; Small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- MG
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Precursor form of the hepatitis delta virus ribozyme | rna | 73 | — | — |
| P | Small nuclear ribonucleoprotein a | protein | 95 | 32% helix, 24% strand | P09012 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains R
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 | 379 | 0.60 | 0.77 | 23 | MG |
| 2 | 433 | 0.56 | 0.74 | 28 | empty |
| 3 | 304 | 0.49 | 0.73 | 17 | empty |
| 4 | 103 | 0.41 | 0.77 | 16 | empty |
| 5 | 90 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- R–P · 959 Ų buried · 29 hydrogen bonds · protein-nucleic
Compared structures
- 1SJ3 · Hepatitis Delta Virus Gemonic Ribozyme Precursor, with Mg2+ Bound · the same entry in another collection · chain R against R, 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 1SJ3 · PDBe 1SJ3 · UniProt P09012
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