Research workbench
Crystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265 in complex with lndfh I
Analyse Crystal structure of the carbohydrate-binding domain VP8* of human P[4]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHU
- Type
- protein
- Length
- 317 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- E9BVI9
- Ligands
- GAL, FUC, BGC, NAG
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer capsid protein VP4 | protein | 158 | 8% helix, 58% strand | E9BVI9 |
| B | Outer capsid protein VP4 | protein | 159 | 10% helix, 57% strand | E9BVI9 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.62 | 0.80 | 31 | empty |
| 2 | 68 | 0.28 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 587 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7KHU · Crystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain… · 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 E9BVI9
- Elsewhere: RCSB PDB 7KHU · PDBe 7KHU · UniProt E9BVI9
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