Research workbench
Crystal structure of the avian reovirus inner capsid protein sigmaa
Analyse Crystal structure of the avian reovirus inner capsid protein sigmaa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VAK
- Type
- protein
- Length
- 4,891 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sigma a
- UniProt
- Q9E6F8
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, K, L | Sigma a | protein | 410 | 44% helix, 14% strand | Q9E6F8 |
| B, D, E, H | Sigma a | protein | 409 | 42% helix, 13% strand | Q9E6F8 |
| C, F, J | Sigma a | protein | 404 | 45% helix, 14% strand | Q9E6F8 |
| G | Sigma a | protein | 403 | 45% helix, 12% strand | Q9E6F8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.77 | 0.81 | 91 | empty |
| 2 | 548 | 0.76 | 0.83 | 63 | empty |
| 3 | 607 | 0.76 | 0.82 | 60 | empty |
| 4 | 582 | 0.75 | 0.82 | 61 | empty |
| 5 | 923 | 0.75 | 0.78 | 91 | empty |
Interfaces
17 interfaces between chains.
- A–B · 755 Ų buried · 8 hydrogen bonds · protein-protein
- H–I · 740 Ų buried · 5 hydrogen bonds · protein-protein
- K–L · 729 Ų buried · 5 hydrogen bonds · protein-protein
- J–K · 723 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 703 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2VAK · Crystal structure of the avian reovirus inner capsid protein sigmaA · 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 Q9E6F8
- Elsewhere: RCSB PDB 2VAK · PDBe 2VAK · UniProt Q9E6F8
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