Research workbench
Unassembled ki polyomavirus VP1 pentamer
Analyse Unassembled ki polyomavirus VP1 pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S7V
- Type
- protein
- Length
- 2,615 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein VP1
- UniProt
- A3R4N3
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 10 distinct chains · 3% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein VP1 | protein | 257 | 4% helix, 40% strand | A3R4N3 |
| B | Major capsid protein VP1 | protein | 262 | 3% helix, 40% strand | A3R4N3 |
| C | Major capsid protein VP1 | protein | 268 | 3% helix, 40% strand | A3R4N3 |
| D | Major capsid protein VP1 | protein | 261 | 2% helix, 41% strand | A3R4N3 |
| E | Major capsid protein VP1 | protein | 261 | 3% helix, 39% strand | A3R4N3 |
| F | Major capsid protein VP1 | protein | 266 | 3% helix, 40% strand | A3R4N3 |
| G | Major capsid protein VP1 | protein | 258 | 3% helix, 41% strand | A3R4N3 |
| H | Major capsid protein VP1 | protein | 265 | 3% helix, 40% strand | A3R4N3 |
| I | Major capsid protein VP1 | protein | 256 | 4% helix, 40% strand | A3R4N3 |
| J | Major capsid protein VP1 | protein | 261 | 3% helix, 41% strand | A3R4N3 |
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 913 | 0.79 | 0.81 | 85 | empty |
| 2 | 217 | 0.54 | 0.78 | 32 | empty |
| 3 | 208 | 0.52 | 0.78 | 27 | empty |
| 4 | 203 | 0.51 | 0.77 | 29 | empty |
| 5 | 209 | 0.49 | 0.76 | 29 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1947 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1946 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 1942 Ų buried · 24 hydrogen bonds · protein-protein
- F–G · 1939 Ų buried · 26 hydrogen bonds · protein-protein
- H–I · 1937 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3S7V · Unassembled KI Polyomavirus VP1 Pentamer · 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 A3R4N3
- Elsewhere: RCSB PDB 3S7V · PDBe 3S7V · UniProt A3R4N3
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