Research workbench
The structure of tomato aspermy virus by X-ray crystallography
Analyse The structure of tomato aspermy virus by X-ray crystallography in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LAJ
- Type
- protein + RNA
- Length
- 543 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; 5'-R(*AP*AP*A)-3'
- UniProt
- P23627
- Ligands
- MG, PO4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein | protein | 174 | 10% helix, 29% strand | P23627 |
| B | Capsid protein | protein | 182 | 13% helix, 27% strand | P23627 |
| C | Capsid protein | protein | 184 | 12% helix, 29% strand | P23627 |
| R | 5'-R(*AP*AP*A)-3' | rna | 3 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.72 | 0.98 | 20 | empty |
| 2 | 348 | 0.67 | 0.81 | 50 | empty |
| 3 | 301 | 0.66 | 0.81 | 42 | empty |
| 4 | 212 | 0.64 | 0.83 | 26 | empty |
| 5 | 426 | 0.63 | 0.77 | 39 | empty |
Interfaces
4 interfaces between chains.
- A–B · 327 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 290 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 289 Ų buried · 2 hydrogen bonds · protein-protein
- A–R · 124 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1LAJ · The Structure of Tomato Aspermy Virus by X-Ray Crystallography · 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 P23627
- Elsewhere: RCSB PDB 1LAJ · PDBe 1LAJ · UniProt P23627
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