Research workbench
Murine polyomavirus complexed with a disialylated oligosaccharide
Analyse Murine polyomavirus complexed with a disialylated oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SIE
- Type
- protein
- Length
- 2,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyomavirus coat protein VP1
- UniProt
- P49302
- Ligands
- SIA, NAG, GAL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyomavirus coat protein VP1 | protein | 366 | 8% helix, 31% strand | P49302 |
| B, E | Polyomavirus coat protein VP1 | protein | 367 | 7% helix, 34% strand | P49302 |
| C | Polyomavirus coat protein VP1 | protein | 357 | 9% helix, 31% strand | P49302 |
| D | Polyomavirus coat protein VP1 | protein | 340 | 9% helix, 31% strand | P49302 |
| F | Polyomavirus coat protein VP1 | protein | 354 | 7% helix, 32% strand | P49302 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 12 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, C, E
- GAL · beta-D-galactopyranose · sugar · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.76 | 0.83 | 59 | empty |
| 2 | 86 | 0.74 | 0.97 | 25 | empty |
| 3 | 80 | 0.74 | 0.98 | 26 | empty |
| 4 | 916 | 0.74 | 0.77 | 75 | empty |
| 5 | 101 | 0.73 | 0.95 | 25 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2966 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 2696 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2679 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2632 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2592 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1SIE · Murine polyomavirus complexed with a disialylated oligosaccharide · the same entry in another collection · chain D against D, 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 P49302
- Elsewhere: RCSB PDB 1SIE · PDBe 1SIE · UniProt P49302
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