Research workbench
Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine
Analyse Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FMI
- Type
- protein
- Length
- 5,474 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- C0JPK1
- Ligands
- SIA, GAL, NAG, CL
- Pockets
- 20 · best druggability 0.66
Structure
x-ray diffraction · 16 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 270 | 9% helix, 39% strand | C0JPK1 |
| B | VP1 | protein | 279 | 9% helix, 38% strand | C0JPK1 |
| C | VP1 | protein | 279 | 8% helix, 38% strand | C0JPK1 |
| D | VP1 | protein | 270 | 9% helix, 40% strand | C0JPK1 |
| E, S | VP1 | protein | 271 | 8% helix, 40% strand | C0JPK1 |
| F | VP1 | protein | 272 | 8% helix, 39% strand | C0JPK1 |
| G | VP1 | protein | 274 | 8% helix, 39% strand | C0JPK1 |
| H | VP1 | protein | 280 | 10% helix, 38% strand | C0JPK1 |
| I | VP1 | protein | 270 | 9% helix, 39% strand | C0JPK1 |
| J, O | VP1 | protein | 271 | 8% helix, 39% strand | C0JPK1 |
| K | VP1 | protein | 274 | 9% helix, 39% strand | C0JPK1 |
| L | VP1 | protein | 271 | 8% helix, 39% strand | C0JPK1 |
| M, N, R | VP1 | protein | 278 | 8% helix, 39% strand | C0JPK1 |
| P | VP1 | protein | 273 | 8% helix, 39% strand | C0JPK1 |
| Q | VP1 | protein | 271 | 8% helix, 39% strand | C0JPK1 |
| T | VP1 | protein | 273 | 9% helix, 38% strand | C0JPK1 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, T, E, M
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, T
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar
- CL · Chloride ion · ion · 21 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
- GOL · Glycerol · additive · 25 copies · chains A, B, C, D, E, F, G, H, I, J, K, O, L, M, N, P, Q, R, S, T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.66 | 0.78 | 44 | empty |
| 2 | 485 | 0.62 | 0.76 | 54 | GOL, CL |
| 3 | 214 | 0.55 | 0.79 | 39 | empty |
| 4 | 265 | 0.54 | 0.76 | 29 | CL |
| 5 | 257 | 0.54 | 0.76 | 31 | GOL, CL |
Interfaces
42 interfaces between chains.
- F–J · 2383 Ų buried · 34 hydrogen bonds · protein-protein
- F–G · 2382 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2379 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 2377 Ų buried · 35 hydrogen bonds · protein-protein
- I–J · 2370 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4FMI · Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine · 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 C0JPK1
- Elsewhere: RCSB PDB 4FMI · PDBe 4FMI · UniProt C0JPK1
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