Research workbench
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with 6'-sialyllactose
Analyse Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U61
- Type
- protein
- Length
- 2,674 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP1
- UniProt
- E2ESL7
- Ligands
- SIA, GAL
- 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, I | Structural protein VP1 | protein | 271 | 5% helix, 38% strand | E2ESL7 |
| B, D, F, H | Structural protein VP1 | protein | 264 | 5% helix, 39% strand | E2ESL7 |
| C, G | Structural protein VP1 | protein | 270 | 5% helix, 38% strand | E2ESL7 |
| E | Structural protein VP1 | protein | 272 | 4% helix, 39% strand | E2ESL7 |
| J | Structural protein VP1 | protein | 264 | 5% helix, 39% strand | E2ESL7 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 7 copies · chains A, E, B, C, D, G, H, I, J
- GAL · beta-D-galactopyranose · sugar
- GOL · Glycerol · additive · 4 copies · chains C, D, A, E, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.61 | 0.77 | 41 | GOL |
| 2 | 422 | 0.55 | 0.73 | 52 | empty |
| 3 | 114 | 0.52 | 0.82 | 20 | GOL |
| 4 | 142 | 0.51 | 0.80 | 22 | empty |
| 5 | 154 | 0.51 | 0.79 | 25 | empty |
Interfaces
25 interfaces between chains.
- C–D · 2295 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2294 Ų buried · 38 hydrogen bonds · protein-protein
- F–J · 2292 Ų buried · 40 hydrogen bonds · protein-protein
- B–C · 2290 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2288 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 4U61 · Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with… · 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 4U61 · PDBe 4U61 · UniProt E2ESL7
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