Research workbench
Crystal structure of the rotavirus strain ds-1 VP8* core
Analyse Crystal structure of the rotavirus strain ds-1 VP8* core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AEN
- Type
- protein
- Length
- 1,312 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4, VP8* core
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Outer capsid protein VP4, VP8* core | protein | 164 | 8% helix, 56% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains B, A, D, E, H, G
- EOH · Ethanol · additive · 4 copies · chains A, D, B, G, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.71 | 0.77 | 78 | EOH, GOL |
| 2 | 372 | 0.58 | 0.76 | 40 | empty |
| 3 | 324 | 0.57 | 0.76 | 38 | empty |
| 4 | 258 | 0.51 | 0.75 | 31 | empty |
| 5 | 146 | 0.48 | 0.77 | 24 | empty |
Interfaces
9 interfaces between chains.
- E–F · 482 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 443 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 439 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 419 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2AEN · Crystal structure of the rotavirus strain DS-1 VP8* core · 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
- Elsewhere: RCSB PDB 2AEN · PDBe 2AEN
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