Research workbench
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1
Analyse Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U5Z
- Type
- protein
- Length
- 2,653 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP1
- UniProt
- E2ESL7
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 10 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Structural protein VP1 | protein | 271 | 4% helix, 38% strand | E2ESL7 |
| B | Structural protein VP1 | protein | 266 | 5% helix, 39% strand | E2ESL7 |
| C | Structural protein VP1 | protein | 270 | 5% helix, 39% strand | E2ESL7 |
| D | Structural protein VP1 | protein | 263 | 5% helix, 40% strand | E2ESL7 |
| E | Structural protein VP1 | protein | 265 | 4% helix, 39% strand | E2ESL7 |
| F | Structural protein VP1 | protein | 265 | 4% helix, 40% strand | E2ESL7 |
| G | Structural protein VP1 | protein | 265 | 5% helix, 38% strand | E2ESL7 |
| H | Structural protein VP1 | protein | 264 | 5% helix, 39% strand | E2ESL7 |
| I | Structural protein VP1 | protein | 260 | 6% helix, 39% strand | E2ESL7 |
| J | Structural protein VP1 | protein | 264 | 5% helix, 39% strand | E2ESL7 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1075 | 0.71 | 0.75 | 127 | empty |
| 2 | 693 | 0.66 | 0.75 | 79 | empty |
| 3 | 236 | 0.53 | 0.77 | 40 | empty |
| 4 | 229 | 0.53 | 0.77 | 31 | empty |
| 5 | 198 | 0.51 | 0.77 | 36 | empty |
Interfaces
22 interfaces between chains.
- A–E · 2341 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 2305 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2302 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2276 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2274 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 4U5Z · Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 · 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 4U5Z · PDBe 4U5Z · UniProt E2ESL7
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