Research workbench
Structure of sheep polyomavirus VP1 in complex with 6'- sialyllactosamine
Analyse Structure of sheep polyomavirus VP1 in complex with 6'- sialyllactosamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y64
- Type
- protein
- Length
- 2,538 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- A0A0E3ZCF3
- Ligands
- SIA, GAL, NAG, MG
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 8 distinct chains · 8% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | Capsid protein VP1 | protein | 257 | 8% helix, 40% strand | A0A0E3ZCF3 |
| B | Capsid protein VP1 | protein | 250 | 8% helix, 40% strand | A0A0E3ZCF3 |
| C, E | Capsid protein VP1 | protein | 258 | 7% helix, 41% strand | A0A0E3ZCF3 |
| D | Capsid protein VP1 | protein | 248 | 8% helix, 41% strand | A0A0E3ZCF3 |
| F | Capsid protein VP1 | protein | 258 | 8% helix, 40% strand | A0A0E3ZCF3 |
| G | Capsid protein VP1 | protein | 249 | 8% helix, 41% strand | A0A0E3ZCF3 |
| I | Capsid protein VP1 | protein | 254 | 8% helix, 40% strand | A0A0E3ZCF3 |
| J | Capsid protein VP1 | protein | 249 | 8% helix, 41% strand | A0A0E3ZCF3 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains C, D, F, J, G, I, A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G
- MG · Magnesium ion · metal · 14 copies · chains A, B, E, C, D, F, G, J, H, I
- GOL · Glycerol · additive · 20 copies · chains A, E, B, D, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 475 | 0.62 | 0.75 | 69 | GOL |
| 2 | 252 | 0.58 | 0.79 | 36 | GOL |
| 3 | 385 | 0.56 | 0.74 | 63 | empty |
| 4 | 61 | 0.54 | 0.88 | 19 | empty |
| 5 | 259 | 0.53 | 0.76 | 37 | GOL |
Interfaces
15 interfaces between chains.
- C–D · 2389 Ų buried · 49 hydrogen bonds · protein-protein
- I–J · 2388 Ų buried · 47 hydrogen bonds · protein-protein
- F–J · 2374 Ų buried · 44 hydrogen bonds · protein-protein
- H–I · 2369 Ų buried · 45 hydrogen bonds · protein-protein
- A–E · 2342 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6Y64 · Structure of Sheep Polyomavirus VP1 in complex with 6'-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 A0A0E3ZCF3
- Elsewhere: RCSB PDB 6Y64 · PDBe 6Y64 · UniProt A0A0E3ZCF3
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