Research workbench
Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scfv 3E8, an astrovirus-neutralizing antibody, at 2.05-a resolution
Analyse Crystal structure of the human astrovirus serotype 8 capsid spike in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RK1
- Type
- protein
- Length
- 882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid polyprotein VP70; Scfv 3E8
- UniProt
- Q9IFX1
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 2% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid polyprotein VP70 | protein | 218 | 0% helix, 47% strand | Q9IFX1 |
| C | Scfv 3E8 | protein | 225 | 4% helix, 50% strand | — |
| B | Capsid polyprotein VP70 | protein | 218 | 0% helix, 47% strand | Q9IFX1 |
| D | Scfv 3E8 | protein | 221 | 5% helix, 50% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.67 | 0.83 | 37 | empty |
| 2 | 136 | 0.54 | 0.82 | 33 | empty |
| 3 | 87 | 0.51 | 0.83 | 20 | empty |
| 4 | 63 | 0.41 | 0.81 | 17 | empty |
| 5 | 105 | 0.37 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1835 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 834 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 826 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7RK1 · Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv… · 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 Q9IFX1
- Elsewhere: RCSB PDB 7RK1 · PDBe 7RK1 · UniProt Q9IFX1
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