MolNFT v1 · #137307 · protein
Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2
5VKI · Outer capsid protein VP4: “Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2”. X-ray diffraction, 5 ligands (THR, NGA, GAL), 1 pocket (best druggability 0.67). MolNFT v1 #137307 on GenesisL1: 3D structure…
- PDB
- 5VKI
- Type
- protein
- Length
- 320 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP4
- UniProt
- A7YCM0
- Ligands
- THR, NGA, GAL, NAG, SO4
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer capsid protein VP4 | protein | 160 | 8% helix, 57% strand | A7YCM0 |
Ligands and binding sites
- THR · Threonine · ligand · 2 copies
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.67 | 0.84 | 45 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5VKI · Crystal structure of P[19] rotavirus VP8* complexed with mucin core 2 · 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 A7YCM0
- Elsewhere: RCSB PDB 5VKI · PDBe 5VKI · UniProt A7YCM0
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