MolNFT v1 · #107291 · protein
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with GM1 oligosaccharide
4U60 · Structural protein VP1: “Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with GM1 oligosaccharide”. X-ray diffraction, 4 ligands (GAL, SIA, NGA), 17 pockets (best druggability 0.53). MolNFT v1 #107291 on…
- PDB
- 4U60
- Type
- protein
- Length
- 1,346 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP1
- UniProt
- E2ESL7
- Ligands
- GAL, SIA, NGA, BGC
- Pockets
- 17 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Structural protein VP1 | protein | 271 | 5% helix, 38% strand | E2ESL7 |
| B | Structural protein VP1 | protein | 262 | 5% helix, 39% strand | E2ESL7 |
| C | Structural protein VP1 | protein | 274 | 5% helix, 38% strand | E2ESL7 |
| D | Structural protein VP1 | protein | 268 | 5% helix, 39% strand | E2ESL7 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains C, D, E
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 5 copies · chains A, E, B, C, D
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains D
- BGC · beta-D-glucopyranose · sugar · 2 copies
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.53 | 0.81 | 23 | GOL |
| 2 | 123 | 0.53 | 0.81 | 22 | GOL |
| 3 | 142 | 0.51 | 0.79 | 25 | GOL |
| 4 | 222 | 0.50 | 0.76 | 28 | empty |
| 5 | 145 | 0.50 | 0.79 | 24 | GOL |
Interfaces
10 interfaces between chains.
- B–C · 2433 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 2321 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2306 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2289 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2274 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 4U60 · Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with GM1… · 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 4U60 · PDBe 4U60 · UniProt E2ESL7
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