MolNFT v1 · #152753 · protein
P domain of GII.3-TV24 with a-tetrasaccharide complex
6IS5 · VP1 capsid protein: “P domain of GII.3-TV24 with a-tetrasaccharide complex”. X-ray diffraction, 4 ligands (GLC, GAL, FUC), 11 pockets (best druggability 0.78). MolNFT v1 #152753 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6IS5
- Type
- protein
- Length
- 1,209 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 capsid protein
- UniProt
- Q66296
- Ligands
- GLC, GAL, FUC, A2G
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | VP1 capsid protein | protein | 301 | 7% helix, 35% strand | Q66296 |
| B | VP1 capsid protein | protein | 304 | 7% helix, 36% strand | Q66296 |
| D | VP1 capsid protein | protein | 303 | 6% helix, 36% strand | Q66296 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B, D, C
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains B, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.78 | 0.80 | 141 | empty |
| 2 | 600 | 0.76 | 0.83 | 94 | empty |
| 3 | 186 | 0.69 | 0.87 | 27 | empty |
| 4 | 182 | 0.67 | 0.86 | 28 | empty |
| 5 | 109 | 0.60 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1803 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1796 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 706 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6IS5 · P domain of GII.3-TV24 with A-tetrasaccharide complex · 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 Q66296
- Elsewhere: RCSB PDB 6IS5 · PDBe 6IS5 · UniProt Q66296
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.