Research workbench
Satellite tobacco mosaic virus refined to 1.4 a resolution using icosahedral constraints
Analyse Satellite tobacco mosaic virus refined to 1.4 a resolution using icosahedral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OQ8
- Type
- protein + RNA
- Length
- 165 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'); RNA…
- UniProt
- P17574
- Ligands
- MG, SO4, PO4
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coat protein | protein | 144 | 7% helix, 40% strand | P17574 |
| B | RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 10 | — | — |
| C | RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') | rna | 10 | — | — |
| D | RNA (5'-R(P*UP*U)-3') | rna | 1 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.51 | 0.85 | 16 | empty |
| 2 | 251 | 0.50 | 0.76 | 17 | empty |
| 3 | 112 | 0.41 | 0.77 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 508 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 196 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 143 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–D · 115 Ų buried · 0 hydrogen bonds · protein-nucleic
- C–D · 87 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Compared structures
- 4OQ8 · Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using icosahedral constraints · 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
- Every structure of UniProt P17574
- Elsewhere: RCSB PDB 4OQ8 · PDBe 4OQ8 · UniProt P17574
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