MolNFT v1 · #103297 · protein
Structure of human polyomavirus 7 (HPYV7) VP1 pentamer
4PCH: “Structure of human polyomavirus 7 (HPYV7) VP1 pentamer”. X-ray diffraction, 16 pockets (best druggability 0.71). MolNFT v1 #103297 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PCH
- Type
- protein
- Length
- 1,294 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1
- UniProt
- D6QWK5
- Pockets
- 16 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 | protein | 252 | 5% helix, 42% strand | D6QWK5 |
| B | VP1 | protein | 266 | 5% helix, 44% strand | D6QWK5 |
| C | VP1 | protein | 265 | 6% helix, 45% strand | D6QWK5 |
| D | VP1 | protein | 248 | 5% helix, 44% strand | D6QWK5 |
| E | VP1 | protein | 263 | 5% helix, 44% strand | D6QWK5 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.71 | 0.76 | 77 | GOL |
| 2 | 193 | 0.48 | 0.77 | 27 | empty |
| 3 | 170 | 0.47 | 0.76 | 24 | empty |
| 4 | 155 | 0.47 | 0.77 | 22 | empty |
| 5 | 167 | 0.46 | 0.76 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2035 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1999 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 1979 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1970 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1959 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 4PCH · Structure of Human Polyomavirus 7 (HPyV7) 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 D6QWK5
- Elsewhere: RCSB PDB 4PCH · PDBe 4PCH · UniProt D6QWK5
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