Research workbench
Unliganded bk polyomavirus VP1 pentamer
Analyse Unliganded bk 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
- 4MJ1
- Type
- protein
- Length
- 1,282 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1 capsid protein
- UniProt
- Q85235
- Ligands
- CL
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 capsid protein | protein | 259 | 7% helix, 42% strand | Q85235 |
| B | VP1 capsid protein | protein | 255 | 7% helix, 42% strand | Q85235 |
| C | VP1 capsid protein | protein | 243 | 7% helix, 42% strand | Q85235 |
| D | VP1 capsid protein | protein | 266 | 8% helix, 42% strand | Q85235 |
| E | VP1 capsid protein | protein | 259 | 7% helix, 43% strand | Q85235 |
Ligands and binding sites
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.63 | 0.74 | 66 | GOL |
| 2 | 359 | 0.58 | 0.76 | 50 | GOL |
| 3 | 308 | 0.54 | 0.75 | 40 | empty |
| 4 | 211 | 0.48 | 0.75 | 27 | GOL |
| 5 | 231 | 0.48 | 0.74 | 26 | GOL |
Interfaces
5 interfaces between chains.
- B–C · 2315 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 2283 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2278 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2270 Ų buried · 39 hydrogen bonds · protein-protein
- D–E · 2245 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4MJ1 · unliganded BK 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 Q85235
- Elsewhere: RCSB PDB 4MJ1 · PDBe 4MJ1 · UniProt Q85235
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