MolNFT v1 · #151335 · protein
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with sialylated precision glycooligomers
6HKU · Capsid protein VP1: “Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with sialylated precision…”. X-ray diffraction, 3 ligands (SIA, GAL, GLC), 20 pockets (best druggability 0.61). MolNFT v1 #151335 on…
- PDB
- 6HKU
- Type
- protein
- Length
- 2,695 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- E2ESL7
- Ligands
- SIA, GAL, GLC
- Pockets
- 20 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, I | Capsid protein VP1 | protein | 272 | 5% helix, 38% strand | E2ESL7 |
| B, H | Capsid protein VP1 | protein | 267 | 5% helix, 39% strand | E2ESL7 |
| D | Capsid protein VP1 | protein | 264 | 5% helix, 39% strand | E2ESL7 |
| E, F, G | Capsid protein VP1 | protein | 271 | 5% helix, 38% strand | E2ESL7 |
| J | Capsid protein VP1 | protein | 268 | 5% helix, 38% strand | E2ESL7 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, F, J, H, I, D
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains C
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C, D
- GOL · Glycerol · additive · 2 copies · chains C, D, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.61 | 0.78 | 31 | GOL |
| 2 | 143 | 0.50 | 0.79 | 22 | empty |
| 3 | 195 | 0.50 | 0.76 | 26 | empty |
| 4 | 193 | 0.49 | 0.77 | 36 | empty |
| 5 | 121 | 0.49 | 0.80 | 23 | empty |
Interfaces
24 interfaces between chains.
- A–B · 2299 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2290 Ų buried · 39 hydrogen bonds · protein-protein
- H–I · 2284 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 2282 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 2281 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6HKU · Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated… · 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 E2ESL7
- Elsewhere: RCSB PDB 6HKU · PDBe 6HKU · UniProt E2ESL7
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