MolNFT v1 · #111085 · protein
Structural basis of glycan recognition in neonate-specific rotaviruses
4YG6 · Outer capsid protein VP8*: “Structural basis of glycan recognition in neonate-specific rotaviruses”. X-ray diffraction, 4 ligands (GAL, NAG, BGC), 3 pockets (best druggability 0.69). MolNFT v1 #111085 on GenesisL1: 3D structure…
- PDB
- 4YG6
- Type
- protein
- Length
- 651 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer capsid protein VP8*
- UniProt
- P35746
- Ligands
- GAL, NAG, BGC, PO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer capsid protein VP8* | protein | 162 | 8% helix, 52% strand | P35746 |
| B, C, D | Outer capsid protein VP8* | protein | 163 | 8% helix, 52% strand | P35746 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 7 copies · chains D, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, B, C
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.69 | 0.79 | 47 | empty |
| 2 | 481 | 0.61 | 0.75 | 51 | NAG, GAL, PO4 |
| 3 | 50 | 0.24 | 0.73 | 12 | empty |
Interfaces
4 interfaces between chains.
- B–D · 617 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 100 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YG6 · Structural basis of glycan recognition in neonate-specific rotaviruses · 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 P35746
- Elsewhere: RCSB PDB 4YG6 · PDBe 4YG6 · UniProt P35746
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