Research workbench
Bk polyomavirus + 20 mm GT1B oligosaccharide
Analyse Bk polyomavirus + 20 mm GT1B oligosaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ESB
- Type
- protein
- Length
- 2,051 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Minor capsid protein VP2
- UniProt
- Q65613, P03094
- Ligands
- SIA, CA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 7 distinct chains · 8% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Capsid protein VP1 | protein | 347 | 5% helix, 30% strand | Q65613 |
| 2 | Capsid protein VP1 | protein | 346 | 8% helix, 34% strand | Q65613 |
| 3 | Capsid protein VP1 | protein | 343 | 8% helix, 30% strand | Q65613 |
| 4 | Capsid protein VP1 | protein | 318 | 9% helix, 32% strand | Q65613 |
| 5 | Capsid protein VP1 | protein | 338 | 10% helix, 29% strand | Q65613 |
| 6 | Capsid protein VP1 | protein | 345 | 8% helix, 31% strand | Q65613 |
| 7 | Minor capsid protein VP2 | protein | 14 | 57% helix, 14% strand | P03094 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 12 copies · chains 1, 5, 2, 3, 4, 6
- CA · Calcium ion · metal · 6 copies · chains 1, 5, 2, 3, 6, 4
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.79 | 0.88 | 44 | empty |
| 2 | 908 | 0.76 | 0.79 | 80 | CA |
| 3 | 867 | 0.75 | 0.79 | 85 | CA |
| 4 | 940 | 0.73 | 0.77 | 88 | CA |
| 5 | 920 | 0.73 | 0.77 | 89 | CA |
Interfaces
8 interfaces between chains.
- 2–3 · 3290 Ų buried · 35 hydrogen bonds · protein-protein
- 1–2 · 2759 Ų buried · 38 hydrogen bonds · protein-protein
- 4–5 · 2661 Ų buried · 42 hydrogen bonds · protein-protein
- 3–4 · 2645 Ų buried · 39 hydrogen bonds · protein-protein
- 2–6 · 2503 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 6ESB · BK polyomavirus + 20 mM GT1b oligosaccharide · the same entry in another collection · chain 1 against 1, 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 Q65613
- Every structure of UniProt P03094
- Elsewhere: RCSB PDB 6ESB · PDBe 6ESB · UniProt Q65613 · UniProt P03094
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