Research workbench
Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with sialylated precision glycooligomers
Analyse Trichodysplasia spinulosa-associated polyomavirus (tspyv) VP1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HKV
- Type
- protein
- Length
- 2,679 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1
- UniProt
- E2ESL7
- Ligands
- GXB, MG, CL
- Pockets
- 20 · best druggability 0.55
Structure
x-ray diffraction · 9 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 271 | 6% helix, 38% strand | E2ESL7 |
| B | Capsid protein VP1 | protein | 265 | 5% helix, 38% strand | E2ESL7 |
| C, F | Capsid protein VP1 | protein | 272 | 5% helix, 38% strand | E2ESL7 |
| D | Capsid protein VP1 | protein | 263 | 5% helix, 39% strand | E2ESL7 |
| E | Capsid protein VP1 | protein | 266 | 4% helix, 40% strand | E2ESL7 |
| G | Capsid protein VP1 | protein | 271 | 4% helix, 39% strand | E2ESL7 |
| H | Capsid protein VP1 | protein | 265 | 5% helix, 39% strand | E2ESL7 |
| I | Capsid protein VP1 | protein | 268 | 6% helix, 38% strand | E2ESL7 |
| J | Capsid protein VP1 | protein | 266 | 5% helix, 38% strand | E2ESL7 |
Ligands and binding sites
- GXB · Sialylated precision glycomacromolecule · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- MG · Magnesium ion · metal · 2 copies · chains C, D, F, G
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · chains E
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 | 430 | 0.55 | 0.73 | 53 | empty |
| 2 | 235 | 0.54 | 0.77 | 26 | empty |
| 3 | 137 | 0.53 | 0.81 | 21 | empty |
| 4 | 138 | 0.51 | 0.80 | 23 | empty |
| 5 | 219 | 0.51 | 0.76 | 40 | empty |
Interfaces
25 interfaces between chains.
- A–B · 2317 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2299 Ų buried · 39 hydrogen bonds · protein-protein
- F–G · 2297 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 2293 Ų buried · 40 hydrogen bonds · protein-protein
- I–J · 2281 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6HKV · Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated… · the same entry in another collection · chain F against F, 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 6HKV · PDBe 6HKV · UniProt E2ESL7
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