Research workbench
Crystal structure of the human astrovirus 2 capsid protein spike domain at 1.87-a resolution
Analyse Crystal structure of the human astrovirus 2 capsid protein spike domain at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KOU
- Type
- protein
- Length
- 877 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid polyprotein VP25
- UniProt
- Q82446
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid polyprotein VP25 | protein | 216 | 3% helix, 48% strand | Q82446 |
| B | Capsid polyprotein VP25 | protein | 225 | 3% helix, 45% strand | Q82446 |
| C | Capsid polyprotein VP25 | protein | 219 | 1% helix, 45% strand | Q82446 |
| D | Capsid polyprotein VP25 | protein | 217 | 1% helix, 47% strand | Q82446 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.69 | 0.77 | 68 | empty |
| 2 | 203 | 0.65 | 0.84 | 40 | empty |
| 3 | 111 | 0.54 | 0.83 | 25 | empty |
| 4 | 84 | 0.54 | 0.85 | 23 | empty |
| 5 | 75 | 0.32 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2015 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 1949 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 187 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5KOU · Crystal structure of the human astrovirus 2 capsid protein spike domain at 1.87-A… · 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 Q82446
- Elsewhere: RCSB PDB 5KOU · PDBe 5KOU · UniProt Q82446
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