Research workbench
Crystal structure of the carbohydrate-binding domain VP8* of human P[8] rotavirus strain BM13851
Analyse Crystal structure of the carbohydrate-binding domain VP8* of human P[8]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKX
- Type
- protein
- Length
- 469 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- M4VSS2
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Outer capsid protein VP4 | protein | 157 | 8% helix, 57% strand | M4VSS2 |
| B | Outer capsid protein VP4 | protein | 155 | 5% helix, 55% strand | M4VSS2 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, C
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 | 514 | 0.69 | 0.79 | 46 | PG4 |
| 2 | 68 | 0.32 | 0.75 | 16 | PEG |
Interfaces
2 interfaces between chains.
- A–B · 316 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VKX · Crystal structure of the carbohydrate-binding domain VP8* of human P[8] 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 M4VSS2
- Elsewhere: RCSB PDB 6VKX · PDBe 6VKX · UniProt M4VSS2
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