MolNFT v1 · #107293 · protein
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with 3'-sialyllactose
4U62 · Structural protein VP1: “Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with 3'-sialyllactose”. X-ray diffraction, 1 ligand (SIA), 20 pockets (best druggability 0.55). MolNFT v1 #107293 on GenesisL1: 3D…
- PDB
- 4U62
- Type
- protein
- Length
- 2,695 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural protein VP1
- UniProt
- E2ESL7
- Ligands
- SIA
- Pockets
- 20 · best druggability 0.55
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H | Structural protein VP1 | protein | 272 | 5% helix, 38% strand | E2ESL7 |
| C | Structural protein VP1 | protein | 268 | 5% helix, 39% strand | E2ESL7 |
| D | Structural protein VP1 | protein | 270 | 5% helix, 39% strand | E2ESL7 |
| E, J | Structural protein VP1 | protein | 271 | 5% helix, 39% strand | E2ESL7 |
| F | Structural protein VP1 | protein | 266 | 5% helix, 39% strand | E2ESL7 |
| G | Structural protein VP1 | protein | 267 | 5% helix, 39% strand | E2ESL7 |
| I | Structural protein VP1 | protein | 266 | 5% helix, 40% strand | E2ESL7 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C, I, J
- GOL · Glycerol · additive · 7 copies · chains A, B, C, E, D, H, I, J, F
- EDO · 1,2-ethanediol · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.55 | 0.74 | 44 | empty |
| 2 | 160 | 0.51 | 0.79 | 25 | GOL |
| 3 | 208 | 0.51 | 0.77 | 38 | empty |
| 4 | 200 | 0.51 | 0.77 | 37 | empty |
| 5 | 120 | 0.51 | 0.81 | 20 | empty |
Interfaces
23 interfaces between chains.
- F–J · 2525 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2408 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2304 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2296 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 2292 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 4U62 · 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 4U62 · PDBe 4U62 · UniProt E2ESL7
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